Starting phenix.real_space_refine on Thu Jul 25 23:14:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8keg_37155/07_2024/8keg_37155_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8keg_37155/07_2024/8keg_37155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8keg_37155/07_2024/8keg_37155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8keg_37155/07_2024/8keg_37155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8keg_37155/07_2024/8keg_37155_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8keg_37155/07_2024/8keg_37155_neut.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 19620 2.51 5 N 5070 2.21 5 O 6165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 131": "OD1" <-> "OD2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 21": "OD1" <-> "OD2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O GLU 110": "OE1" <-> "OE2" Residue "a PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 117": "OD1" <-> "OD2" Residue "j PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30930 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "C" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "D" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "E" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "F" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "G" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "H" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "J" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "K" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "L" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "M" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "N" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "O" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "a" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "b" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "c" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "e" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "f" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "g" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "h" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "i" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "j" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "k" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "l" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "m" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "n" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "o" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Time building chain proxies: 18.82, per 1000 atoms: 0.61 Number of scatterers: 30930 At special positions: 0 Unit cell: (218.28, 209.72, 82.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 6165 8.00 N 5070 7.00 C 19620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.45 Conformation dependent library (CDL) restraints added in 5.4 seconds 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7380 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 52 sheets defined 41.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.974A pdb=" N PHE A 19 " --> pdb=" O TYR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 57 through 82 removed outlier: 3.910A pdb=" N ILE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 119 Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 57 through 84 removed outlier: 3.673A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 Processing helix chain 'C' and resid 10 through 19 removed outlier: 4.070A pdb=" N PHE C 19 " --> pdb=" O TYR C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.779A pdb=" N ALA C 52 " --> pdb=" O ASN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 82 removed outlier: 3.849A pdb=" N ILE C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 118 Processing helix chain 'D' and resid 10 through 18 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 46 through 54 removed outlier: 4.242A pdb=" N ALA D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 82 removed outlier: 3.819A pdb=" N ILE D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 118 removed outlier: 3.542A pdb=" N LEU D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 18 removed outlier: 3.808A pdb=" N GLN E 18 " --> pdb=" O SER E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 40 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 57 through 84 removed outlier: 3.780A pdb=" N LYS E 79 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 119 Processing helix chain 'F' and resid 10 through 18 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 57 through 82 removed outlier: 3.927A pdb=" N ILE F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 118 removed outlier: 3.507A pdb=" N LEU F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 19 removed outlier: 3.872A pdb=" N PHE G 19 " --> pdb=" O TYR G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 41 Processing helix chain 'G' and resid 46 through 54 removed outlier: 4.142A pdb=" N ALA G 52 " --> pdb=" O ASN G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 82 removed outlier: 3.876A pdb=" N ILE G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 118 Processing helix chain 'H' and resid 10 through 17 Processing helix chain 'H' and resid 29 through 40 Processing helix chain 'H' and resid 46 through 54 Processing helix chain 'H' and resid 57 through 82 Processing helix chain 'H' and resid 98 through 118 Processing helix chain 'I' and resid 10 through 18 Processing helix chain 'I' and resid 29 through 41 Processing helix chain 'I' and resid 46 through 54 Processing helix chain 'I' and resid 57 through 83 removed outlier: 3.588A pdb=" N LYS I 79 " --> pdb=" O ASP I 75 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE I 82 " --> pdb=" O ASN I 78 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU I 83 " --> pdb=" O LYS I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 118 Processing helix chain 'J' and resid 10 through 19 removed outlier: 3.805A pdb=" N PHE J 19 " --> pdb=" O TYR J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 41 Processing helix chain 'J' and resid 46 through 54 removed outlier: 4.199A pdb=" N ALA J 52 " --> pdb=" O ASN J 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU J 53 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 82 removed outlier: 3.591A pdb=" N ILE J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 118 Processing helix chain 'K' and resid 10 through 17 Processing helix chain 'K' and resid 29 through 40 Processing helix chain 'K' and resid 46 through 54 Processing helix chain 'K' and resid 57 through 82 removed outlier: 3.559A pdb=" N LYS K 79 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 118 Processing helix chain 'L' and resid 10 through 18 Processing helix chain 'L' and resid 29 through 41 Processing helix chain 'L' and resid 46 through 54 Processing helix chain 'L' and resid 57 through 82 removed outlier: 3.912A pdb=" N ILE L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 118 Processing helix chain 'M' and resid 10 through 18 Processing helix chain 'M' and resid 29 through 41 Processing helix chain 'M' and resid 48 through 55 Processing helix chain 'M' and resid 57 through 82 removed outlier: 3.667A pdb=" N ILE M 82 " --> pdb=" O ASN M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 118 Processing helix chain 'N' and resid 10 through 17 Processing helix chain 'N' and resid 29 through 41 Processing helix chain 'N' and resid 46 through 54 removed outlier: 3.729A pdb=" N ALA N 52 " --> pdb=" O ASN N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 82 removed outlier: 3.553A pdb=" N LYS N 79 " --> pdb=" O ASP N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 119 Processing helix chain 'O' and resid 10 through 18 Processing helix chain 'O' and resid 29 through 41 Processing helix chain 'O' and resid 46 through 54 Processing helix chain 'O' and resid 57 through 82 removed outlier: 4.004A pdb=" N ILE O 82 " --> pdb=" O ASN O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 118 Processing helix chain 'a' and resid 88 through 95 removed outlier: 3.626A pdb=" N VAL a 92 " --> pdb=" O GLU a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 125 Processing helix chain 'b' and resid 89 through 94 Processing helix chain 'b' and resid 101 through 106 removed outlier: 4.117A pdb=" N ASN b 106 " --> pdb=" O GLU b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 124 removed outlier: 4.776A pdb=" N ASP b 113 " --> pdb=" O ASN b 109 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN b 121 " --> pdb=" O ASP b 117 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE b 122 " --> pdb=" O ALA b 118 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN b 123 " --> pdb=" O ILE b 119 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA b 124 " --> pdb=" O ALA b 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 89 through 96 Processing helix chain 'c' and resid 97 through 99 No H-bonds generated for 'chain 'c' and resid 97 through 99' Processing helix chain 'c' and resid 106 through 123 Processing helix chain 'd' and resid 88 through 95 removed outlier: 3.600A pdb=" N VAL d 92 " --> pdb=" O GLU d 88 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA d 95 " --> pdb=" O VAL d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 125 Processing helix chain 'e' and resid 89 through 96 Processing helix chain 'e' and resid 110 through 123 Processing helix chain 'f' and resid 89 through 96 Processing helix chain 'f' and resid 97 through 99 No H-bonds generated for 'chain 'f' and resid 97 through 99' Processing helix chain 'f' and resid 104 through 125 removed outlier: 4.247A pdb=" N LEU f 108 " --> pdb=" O TYR f 104 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER f 125 " --> pdb=" O ASN f 121 " (cutoff:3.500A) Processing helix chain 'g' and resid 88 through 95 removed outlier: 4.070A pdb=" N VAL g 92 " --> pdb=" O GLU g 88 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA g 95 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 105 through 123 removed outlier: 4.299A pdb=" N GLN g 123 " --> pdb=" O ILE g 119 " (cutoff:3.500A) Processing helix chain 'h' and resid 89 through 94 Processing helix chain 'h' and resid 107 through 125 removed outlier: 4.074A pdb=" N SER h 125 " --> pdb=" O ASN h 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 89 through 96 Processing helix chain 'i' and resid 97 through 99 No H-bonds generated for 'chain 'i' and resid 97 through 99' Processing helix chain 'i' and resid 104 through 125 Processing helix chain 'j' and resid 88 through 95 removed outlier: 3.908A pdb=" N VAL j 92 " --> pdb=" O GLU j 88 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 125 Processing helix chain 'k' and resid 89 through 94 Processing helix chain 'k' and resid 104 through 125 removed outlier: 4.011A pdb=" N LEU k 108 " --> pdb=" O TYR k 104 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER k 125 " --> pdb=" O ASN k 121 " (cutoff:3.500A) Processing helix chain 'l' and resid 89 through 96 Processing helix chain 'l' and resid 105 through 124 Processing helix chain 'm' and resid 88 through 95 removed outlier: 3.782A pdb=" N VAL m 92 " --> pdb=" O GLU m 88 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA m 95 " --> pdb=" O VAL m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 104 through 124 Processing helix chain 'n' and resid 89 through 93 Processing helix chain 'n' and resid 104 through 124 Processing helix chain 'o' and resid 89 through 96 Processing helix chain 'o' and resid 97 through 100 removed outlier: 3.579A pdb=" N THR o 100 " --> pdb=" O ILE o 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 100' Processing helix chain 'o' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA2, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AA3, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AA4, first strand: chain 'H' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AA6, first strand: chain 'L' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'M' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'a' and resid 2 through 3 Processing sheet with id=AA9, first strand: chain 'a' and resid 40 through 44 Processing sheet with id=AB1, first strand: chain 'a' and resid 29 through 30 Processing sheet with id=AB2, first strand: chain 'b' and resid 50 through 55 removed outlier: 5.624A pdb=" N ARG b 3 " --> pdb=" O ILE b 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 40 through 44 Processing sheet with id=AB4, first strand: chain 'b' and resid 29 through 30 Processing sheet with id=AB5, first strand: chain 'c' and resid 50 through 54 Processing sheet with id=AB6, first strand: chain 'c' and resid 40 through 44 Processing sheet with id=AB7, first strand: chain 'c' and resid 29 through 30 Processing sheet with id=AB8, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AB9, first strand: chain 'd' and resid 6 through 7 Processing sheet with id=AC1, first strand: chain 'd' and resid 40 through 44 Processing sheet with id=AC2, first strand: chain 'd' and resid 29 through 30 Processing sheet with id=AC3, first strand: chain 'e' and resid 50 through 55 removed outlier: 5.901A pdb=" N ARG e 3 " --> pdb=" O ILE e 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 40 through 44 Processing sheet with id=AC5, first strand: chain 'e' and resid 29 through 30 Processing sheet with id=AC6, first strand: chain 'f' and resid 50 through 55 Processing sheet with id=AC7, first strand: chain 'f' and resid 40 through 44 Processing sheet with id=AC8, first strand: chain 'f' and resid 29 through 30 Processing sheet with id=AC9, first strand: chain 'g' and resid 6 through 7 Processing sheet with id=AD1, first strand: chain 'g' and resid 40 through 44 Processing sheet with id=AD2, first strand: chain 'g' and resid 29 through 30 Processing sheet with id=AD3, first strand: chain 'h' and resid 50 through 55 Processing sheet with id=AD4, first strand: chain 'h' and resid 40 through 44 removed outlier: 3.644A pdb=" N PHE h 22 " --> pdb=" O THR h 69 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR h 65 " --> pdb=" O ILE h 26 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'h' and resid 29 through 30 Processing sheet with id=AD6, first strand: chain 'i' and resid 50 through 55 Processing sheet with id=AD7, first strand: chain 'i' and resid 40 through 44 Processing sheet with id=AD8, first strand: chain 'i' and resid 29 through 31 Processing sheet with id=AD9, first strand: chain 'j' and resid 40 through 44 Processing sheet with id=AE1, first strand: chain 'j' and resid 29 through 31 removed outlier: 3.582A pdb=" N ASN j 34 " --> pdb=" O ASN j 31 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'k' and resid 50 through 54 removed outlier: 5.821A pdb=" N ARG k 3 " --> pdb=" O ILE k 87 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'k' and resid 40 through 44 Processing sheet with id=AE4, first strand: chain 'k' and resid 29 through 31 removed outlier: 3.791A pdb=" N ASN k 34 " --> pdb=" O ASN k 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'l' and resid 50 through 54 removed outlier: 6.207A pdb=" N ARG l 3 " --> pdb=" O ILE l 87 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'l' and resid 40 through 44 removed outlier: 3.516A pdb=" N TYR l 66 " --> pdb=" O PHE l 78 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'l' and resid 29 through 31 Processing sheet with id=AE8, first strand: chain 'm' and resid 6 through 7 Processing sheet with id=AE9, first strand: chain 'm' and resid 40 through 44 Processing sheet with id=AF1, first strand: chain 'm' and resid 29 through 30 Processing sheet with id=AF2, first strand: chain 'n' and resid 50 through 55 Processing sheet with id=AF3, first strand: chain 'n' and resid 40 through 44 Processing sheet with id=AF4, first strand: chain 'n' and resid 29 through 30 Processing sheet with id=AF5, first strand: chain 'o' and resid 50 through 55 Processing sheet with id=AF6, first strand: chain 'o' and resid 40 through 44 Processing sheet with id=AF7, first strand: chain 'o' and resid 29 through 30 1420 hydrogen bonds defined for protein. 4086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.57 Time building geometry restraints manager: 14.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10316 1.34 - 1.46: 4700 1.46 - 1.57: 16319 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 31470 Sorted by residual: bond pdb=" CB GLU g 103 " pdb=" CG GLU g 103 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.08e+00 bond pdb=" N ARG F 136 " pdb=" CA ARG F 136 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C ASP k 101 " pdb=" N PRO k 102 " ideal model delta sigma weight residual 1.331 1.344 -0.013 7.90e-03 1.60e+04 2.68e+00 bond pdb=" CA ILE F 93 " pdb=" CB ILE F 93 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.05e-02 9.07e+03 2.10e+00 bond pdb=" CA ASP f 101 " pdb=" C ASP f 101 " ideal model delta sigma weight residual 1.534 1.521 0.013 9.50e-03 1.11e+04 2.02e+00 ... (remaining 31465 not shown) Histogram of bond angle deviations from ideal: 99.27 - 108.02: 1049 108.02 - 116.77: 21158 116.77 - 125.52: 20238 125.52 - 134.26: 302 134.26 - 143.01: 33 Bond angle restraints: 42780 Sorted by residual: angle pdb=" C ARG n 93 " pdb=" N GLU n 94 " pdb=" CA GLU n 94 " ideal model delta sigma weight residual 121.14 141.60 -20.46 1.75e+00 3.27e-01 1.37e+02 angle pdb=" C PRO o 57 " pdb=" N ASN o 58 " pdb=" CA ASN o 58 " ideal model delta sigma weight residual 120.60 139.21 -18.61 1.60e+00 3.91e-01 1.35e+02 angle pdb=" C ASP H 124 " pdb=" N ASN H 125 " pdb=" CA ASN H 125 " ideal model delta sigma weight residual 122.11 139.75 -17.64 1.59e+00 3.96e-01 1.23e+02 angle pdb=" C GLU L 134 " pdb=" N GLY L 135 " pdb=" CA GLY L 135 " ideal model delta sigma weight residual 121.41 142.99 -21.58 1.96e+00 2.60e-01 1.21e+02 angle pdb=" C ALA d 95 " pdb=" N GLY d 96 " pdb=" CA GLY d 96 " ideal model delta sigma weight residual 121.41 142.30 -20.89 1.96e+00 2.60e-01 1.14e+02 ... (remaining 42775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 17464 17.97 - 35.93: 1295 35.93 - 53.90: 237 53.90 - 71.87: 63 71.87 - 89.83: 21 Dihedral angle restraints: 19080 sinusoidal: 7695 harmonic: 11385 Sorted by residual: dihedral pdb=" CA PRO i 57 " pdb=" C PRO i 57 " pdb=" N ASN i 58 " pdb=" CA ASN i 58 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ASP l 101 " pdb=" C ASP l 101 " pdb=" N PRO l 102 " pdb=" CA PRO l 102 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C LYS M 89 " pdb=" N LYS M 89 " pdb=" CA LYS M 89 " pdb=" CB LYS M 89 " ideal model delta harmonic sigma weight residual -122.60 -134.52 11.92 0 2.50e+00 1.60e-01 2.27e+01 ... (remaining 19077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 4897 0.348 - 0.697: 70 0.697 - 1.045: 0 1.045 - 1.394: 1 1.394 - 1.742: 27 Chirality restraints: 4995 Sorted by residual: chirality pdb=" CB ILE M 93 " pdb=" CA ILE M 93 " pdb=" CG1 ILE M 93 " pdb=" CG2 ILE M 93 " both_signs ideal model delta sigma weight residual False 2.64 0.90 1.74 2.00e-01 2.50e+01 7.59e+01 chirality pdb=" CB ILE D 93 " pdb=" CA ILE D 93 " pdb=" CG1 ILE D 93 " pdb=" CG2 ILE D 93 " both_signs ideal model delta sigma weight residual False 2.64 0.92 1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" CB ILE J 93 " pdb=" CA ILE J 93 " pdb=" CG1 ILE J 93 " pdb=" CG2 ILE J 93 " both_signs ideal model delta sigma weight residual False 2.64 0.93 1.71 2.00e-01 2.50e+01 7.34e+01 ... (remaining 4992 not shown) Planarity restraints: 5565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 42 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 43 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP a 101 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO a 102 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO a 102 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO a 102 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 23 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO E 24 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 24 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 24 " 0.023 5.00e-02 4.00e+02 ... (remaining 5562 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 682 2.52 - 3.11: 29675 3.11 - 3.71: 52709 3.71 - 4.30: 71241 4.30 - 4.90: 113028 Nonbonded interactions: 267335 Sorted by model distance: nonbonded pdb=" OG1 THR g 70 " pdb=" OD1 ASP g 72 " model vdw 1.923 2.440 nonbonded pdb=" O ILE c 97 " pdb=" OG1 THR c 100 " model vdw 1.947 2.440 nonbonded pdb=" OG1 THR e 70 " pdb=" OD1 ASP e 72 " model vdw 1.948 2.440 nonbonded pdb=" O THR H 88 " pdb=" OG1 THR I 94 " model vdw 1.964 2.440 nonbonded pdb=" O ILE i 97 " pdb=" OG1 THR i 100 " model vdw 1.972 2.440 ... (remaining 267330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 82.880 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31470 Z= 0.206 Angle : 0.887 21.577 42780 Z= 0.486 Chirality : 0.135 1.742 4995 Planarity : 0.004 0.054 5565 Dihedral : 13.566 89.833 11700 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.83 % Favored : 91.04 % Rotamer: Outliers : 4.91 % Allowed : 13.08 % Favored : 82.01 % Cbeta Deviations : 1.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3795 helix: 1.31 (0.13), residues: 1489 sheet: -1.24 (0.21), residues: 569 loop : -2.26 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 16 HIS 0.006 0.001 HIS o 10 PHE 0.009 0.001 PHE I 42 TYR 0.012 0.001 TYR n 104 ARG 0.004 0.001 ARG M 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1282 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.9614 (t80) cc_final: 0.9030 (t80) REVERT: A 38 MET cc_start: 0.8923 (tmm) cc_final: 0.8406 (tmm) REVERT: A 39 CYS cc_start: 0.8889 (p) cc_final: 0.8671 (p) REVERT: A 92 ASP cc_start: 0.8125 (p0) cc_final: 0.7619 (p0) REVERT: A 95 MET cc_start: 0.8632 (mtp) cc_final: 0.8376 (mtm) REVERT: A 102 ASP cc_start: 0.9160 (m-30) cc_final: 0.8805 (m-30) REVERT: A 106 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8474 (mt-10) REVERT: A 122 VAL cc_start: 0.9061 (t) cc_final: 0.8746 (p) REVERT: B 49 PHE cc_start: 0.9700 (t80) cc_final: 0.9348 (t80) REVERT: B 63 THR cc_start: 0.9665 (m) cc_final: 0.9443 (p) REVERT: B 86 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8470 (tm-30) REVERT: B 131 ASP cc_start: 0.8632 (t0) cc_final: 0.8386 (t0) REVERT: C 13 GLU cc_start: 0.8468 (tp30) cc_final: 0.7788 (tp30) REVERT: C 17 ASN cc_start: 0.9155 (m-40) cc_final: 0.8374 (m-40) REVERT: C 19 PHE cc_start: 0.8654 (m-80) cc_final: 0.8447 (m-80) REVERT: C 39 CYS cc_start: 0.9149 (p) cc_final: 0.8713 (p) REVERT: C 70 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8536 (mm-30) REVERT: C 92 ASP cc_start: 0.7616 (p0) cc_final: 0.6913 (p0) REVERT: C 105 ASP cc_start: 0.9342 (m-30) cc_final: 0.9107 (m-30) REVERT: C 124 ASP cc_start: 0.7955 (t0) cc_final: 0.6499 (t70) REVERT: C 134 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.6058 (tp30) REVERT: D 76 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8679 (mmtm) REVERT: E 49 PHE cc_start: 0.9602 (t80) cc_final: 0.9392 (t80) REVERT: E 89 LYS cc_start: 0.8675 (ptmm) cc_final: 0.7793 (ptmm) REVERT: E 105 ASP cc_start: 0.9223 (m-30) cc_final: 0.9018 (m-30) REVERT: F 38 MET cc_start: 0.8573 (tmm) cc_final: 0.8342 (tmm) REVERT: F 39 CYS cc_start: 0.9241 (p) cc_final: 0.8849 (p) REVERT: F 60 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8651 (mt-10) REVERT: F 70 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8447 (mm-30) REVERT: F 86 GLN cc_start: 0.9011 (mm110) cc_final: 0.8698 (tp40) REVERT: F 92 ASP cc_start: 0.7255 (t70) cc_final: 0.6598 (t70) REVERT: F 105 ASP cc_start: 0.9338 (m-30) cc_final: 0.9084 (m-30) REVERT: F 110 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8181 (mm-30) REVERT: F 116 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8146 (mmm160) REVERT: G 89 LYS cc_start: 0.9030 (ptmm) cc_final: 0.8776 (ptmm) REVERT: G 110 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8997 (mm-30) REVERT: G 113 LYS cc_start: 0.9455 (mttt) cc_final: 0.9062 (mtmt) REVERT: G 132 ASP cc_start: 0.7431 (m-30) cc_final: 0.7130 (m-30) REVERT: H 38 MET cc_start: 0.9298 (ttp) cc_final: 0.8974 (ttm) REVERT: H 44 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8248 (ptm160) REVERT: H 49 PHE cc_start: 0.9739 (t80) cc_final: 0.9487 (t80) REVERT: H 89 LYS cc_start: 0.8319 (ttmm) cc_final: 0.8010 (ttmm) REVERT: H 92 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7702 (p0) REVERT: H 98 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8818 (p0) REVERT: H 119 LYS cc_start: 0.9488 (mmtm) cc_final: 0.9277 (mmtm) REVERT: H 124 ASP cc_start: 0.8743 (t0) cc_final: 0.8460 (t0) REVERT: I 17 ASN cc_start: 0.9556 (m-40) cc_final: 0.9278 (m-40) REVERT: I 38 MET cc_start: 0.8829 (tmm) cc_final: 0.8491 (tmm) REVERT: I 39 CYS cc_start: 0.9169 (p) cc_final: 0.8561 (p) REVERT: I 83 GLU cc_start: 0.7512 (mp0) cc_final: 0.7309 (mp0) REVERT: I 86 GLN cc_start: 0.8710 (tp40) cc_final: 0.8480 (tp40) REVERT: I 102 ASP cc_start: 0.8914 (m-30) cc_final: 0.8657 (m-30) REVERT: I 106 GLU cc_start: 0.9129 (tp30) cc_final: 0.8865 (mm-30) REVERT: J 13 GLU cc_start: 0.8249 (tp30) cc_final: 0.7999 (tp30) REVERT: J 25 THR cc_start: 0.8230 (p) cc_final: 0.7658 (t) REVERT: J 60 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8363 (mt-10) REVERT: J 70 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8317 (mm-30) REVERT: J 76 LYS cc_start: 0.9440 (tttt) cc_final: 0.9063 (ptmm) REVERT: J 80 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7752 (mt-10) REVERT: J 83 GLU cc_start: 0.7839 (pp20) cc_final: 0.7634 (tm-30) REVERT: J 92 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8371 (p0) REVERT: K 15 TYR cc_start: 0.9002 (t80) cc_final: 0.8701 (t80) REVERT: K 27 GLU cc_start: 0.7915 (pm20) cc_final: 0.7685 (pm20) REVERT: K 29 GLU cc_start: 0.8266 (mp0) cc_final: 0.8050 (mp0) REVERT: K 43 PRO cc_start: 0.9437 (Cg_exo) cc_final: 0.8860 (Cg_endo) REVERT: K 69 LYS cc_start: 0.9715 (tttp) cc_final: 0.9335 (ttmm) REVERT: K 89 LYS cc_start: 0.8877 (ptmm) cc_final: 0.8567 (ptmm) REVERT: K 90 VAL cc_start: 0.8678 (t) cc_final: 0.8467 (t) REVERT: K 116 ARG cc_start: 0.9198 (mmt-90) cc_final: 0.8911 (tpp80) REVERT: L 21 ASP cc_start: 0.7427 (p0) cc_final: 0.6933 (p0) REVERT: L 38 MET cc_start: 0.8776 (tmm) cc_final: 0.8501 (tmm) REVERT: L 39 CYS cc_start: 0.9043 (p) cc_final: 0.8525 (p) REVERT: L 60 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8761 (mt-10) REVERT: L 83 GLU cc_start: 0.8212 (mp0) cc_final: 0.7989 (mp0) REVERT: L 86 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8791 (tp40) REVERT: L 106 GLU cc_start: 0.9131 (tp30) cc_final: 0.8902 (mm-30) REVERT: L 107 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9366 (mp) REVERT: M 15 TYR cc_start: 0.8729 (t80) cc_final: 0.8446 (t80) REVERT: M 70 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8670 (mm-30) REVERT: M 75 ASP cc_start: 0.8602 (p0) cc_final: 0.8393 (p0) REVERT: M 105 ASP cc_start: 0.9074 (m-30) cc_final: 0.8870 (m-30) REVERT: M 131 ASP cc_start: 0.8616 (t0) cc_final: 0.8309 (t0) REVERT: N 15 TYR cc_start: 0.9192 (t80) cc_final: 0.8962 (t80) REVERT: O 13 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8798 (mt-10) REVERT: O 21 ASP cc_start: 0.7556 (p0) cc_final: 0.7191 (p0) REVERT: O 38 MET cc_start: 0.8605 (tmm) cc_final: 0.8373 (tmm) REVERT: O 39 CYS cc_start: 0.9168 (p) cc_final: 0.8904 (p) REVERT: O 60 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8360 (mt-10) REVERT: O 69 LYS cc_start: 0.9539 (ttmt) cc_final: 0.9239 (ttmm) REVERT: O 83 GLU cc_start: 0.7770 (mp0) cc_final: 0.7534 (mp0) REVERT: O 91 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: O 112 LYS cc_start: 0.9488 (ptpp) cc_final: 0.9275 (ptpp) REVERT: O 129 SER cc_start: 0.8657 (p) cc_final: 0.7601 (p) REVERT: O 130 TYR cc_start: 0.7086 (p90) cc_final: 0.6822 (p90) REVERT: a 48 ASN cc_start: 0.9068 (t0) cc_final: 0.8564 (t0) REVERT: a 50 GLU cc_start: 0.8096 (mp0) cc_final: 0.7687 (mp0) REVERT: a 113 ASP cc_start: 0.9100 (t70) cc_final: 0.8899 (t0) REVERT: a 117 ASP cc_start: 0.9289 (m-30) cc_final: 0.9051 (m-30) REVERT: d 18 ASN cc_start: 0.8945 (t0) cc_final: 0.8659 (t0) REVERT: d 48 ASN cc_start: 0.9041 (t0) cc_final: 0.8742 (t0) REVERT: d 82 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: e 14 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: e 16 TRP cc_start: 0.7478 (OUTLIER) cc_final: 0.4707 (m100) REVERT: e 23 LEU cc_start: 0.8021 (tp) cc_final: 0.7820 (tp) REVERT: e 30 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7686 (p90) REVERT: e 36 TYR cc_start: 0.8190 (m-80) cc_final: 0.7974 (m-10) REVERT: e 90 SER cc_start: 0.8610 (t) cc_final: 0.7981 (p) REVERT: e 103 GLU cc_start: -0.2715 (OUTLIER) cc_final: -0.3653 (pt0) REVERT: e 107 VAL cc_start: 0.7132 (t) cc_final: 0.6745 (t) REVERT: e 108 LEU cc_start: 0.8965 (mt) cc_final: 0.8660 (mt) REVERT: f 5 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7429 (mtmm) REVERT: f 17 ILE cc_start: 0.7397 (mp) cc_final: 0.7058 (mm) REVERT: f 27 ASN cc_start: 0.8303 (m-40) cc_final: 0.7595 (m-40) REVERT: f 58 ASN cc_start: 0.5949 (OUTLIER) cc_final: 0.5540 (m110) REVERT: f 64 SER cc_start: 0.6176 (OUTLIER) cc_final: 0.5574 (t) REVERT: f 91 VAL cc_start: 0.9526 (t) cc_final: 0.9194 (m) REVERT: f 109 ASN cc_start: 0.8873 (m-40) cc_final: 0.8512 (m110) REVERT: f 110 TYR cc_start: 0.9138 (t80) cc_final: 0.8837 (t80) REVERT: g 48 ASN cc_start: 0.9035 (t0) cc_final: 0.8791 (t0) REVERT: g 50 GLU cc_start: 0.7993 (mp0) cc_final: 0.7743 (mp0) REVERT: g 68 LEU cc_start: 0.9376 (tt) cc_final: 0.9168 (tt) REVERT: g 91 VAL cc_start: 0.8721 (m) cc_final: 0.8487 (p) REVERT: h 1 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5572 (tmm) REVERT: h 27 ASN cc_start: 0.6243 (t0) cc_final: 0.5895 (t0) REVERT: h 36 TYR cc_start: 0.8519 (m-80) cc_final: 0.8223 (m-80) REVERT: j 12 ASP cc_start: 0.8395 (p0) cc_final: 0.7372 (p0) REVERT: j 48 ASN cc_start: 0.9001 (t0) cc_final: 0.8691 (t0) REVERT: j 50 GLU cc_start: 0.7859 (pm20) cc_final: 0.7336 (pm20) REVERT: j 54 ASN cc_start: 0.7088 (t0) cc_final: 0.6648 (t0) REVERT: j 111 LEU cc_start: 0.9543 (mt) cc_final: 0.9293 (mt) REVERT: j 117 ASP cc_start: 0.8703 (p0) cc_final: 0.8486 (p0) REVERT: k 5 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8420 (mtmm) REVERT: k 25 LEU cc_start: 0.8556 (tp) cc_final: 0.8337 (tp) REVERT: k 58 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.6263 (m-40) REVERT: k 116 ASP cc_start: 0.9462 (m-30) cc_final: 0.9221 (m-30) REVERT: l 77 SER cc_start: 0.9288 (p) cc_final: 0.9076 (t) REVERT: l 94 GLU cc_start: 0.8359 (tp30) cc_final: 0.7884 (tp30) REVERT: l 110 TYR cc_start: 0.8995 (t80) cc_final: 0.8723 (t80) REVERT: m 48 ASN cc_start: 0.8556 (t0) cc_final: 0.8309 (t0) REVERT: m 50 GLU cc_start: 0.7848 (pm20) cc_final: 0.7270 (pm20) REVERT: n 42 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8090 (t70) REVERT: n 59 VAL cc_start: 0.8768 (m) cc_final: 0.8453 (m) REVERT: n 111 LEU cc_start: 0.9388 (mm) cc_final: 0.8868 (pp) outliers start: 173 outliers final: 95 residues processed: 1391 average time/residue: 0.4380 time to fit residues: 941.1797 Evaluate side-chains 1137 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1025 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 130 TYR Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 130 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 125 ASN Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 65 TYR Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 82 ASP Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain f residue 58 ASN Chi-restraints excluded: chain f residue 64 SER Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 112 GLU Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 94 GLU Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 58 ASN Chi-restraints excluded: chain k residue 70 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 293 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 chunk 218 optimal weight: 30.0000 chunk 340 optimal weight: 0.3980 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 86 GLN A 98 ASN C 86 GLN F 86 GLN G 47 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 78 ASN ** a 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN a 58 ASN ** a 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 54 ASN ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 109 ASN ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 73 ASN ** f 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 109 ASN ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 ASN ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 ASN ** i 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 GLN ** k 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 121 ASN ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 58 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 31470 Z= 0.335 Angle : 0.764 9.511 42780 Z= 0.402 Chirality : 0.047 0.229 4995 Planarity : 0.005 0.072 5565 Dihedral : 8.966 88.908 4390 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.91 % Favored : 90.96 % Rotamer: Outliers : 6.75 % Allowed : 18.44 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3795 helix: 0.66 (0.13), residues: 1659 sheet: -0.95 (0.21), residues: 596 loop : -2.47 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP o 16 HIS 0.017 0.002 HIS b 42 PHE 0.026 0.002 PHE I 19 TYR 0.027 0.002 TYR f 36 ARG 0.011 0.001 ARG l 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1134 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8598 (tp30) cc_final: 0.8210 (tp30) REVERT: A 25 THR cc_start: 0.7750 (p) cc_final: 0.7212 (t) REVERT: A 35 PHE cc_start: 0.9661 (t80) cc_final: 0.9101 (t80) REVERT: A 38 MET cc_start: 0.9152 (tmm) cc_final: 0.8529 (tmm) REVERT: A 39 CYS cc_start: 0.8896 (p) cc_final: 0.8639 (p) REVERT: A 70 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8689 (tp30) REVERT: A 92 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8034 (p0) REVERT: A 122 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8595 (m) REVERT: B 44 ARG cc_start: 0.7952 (ptp-170) cc_final: 0.7509 (ttm-80) REVERT: B 49 PHE cc_start: 0.9732 (t80) cc_final: 0.9412 (t80) REVERT: B 86 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8843 (tp-100) REVERT: B 89 LYS cc_start: 0.8693 (tppt) cc_final: 0.8442 (tppt) REVERT: B 131 ASP cc_start: 0.8826 (t0) cc_final: 0.8472 (t0) REVERT: C 13 GLU cc_start: 0.8662 (tp30) cc_final: 0.7574 (tp30) REVERT: C 17 ASN cc_start: 0.9245 (m-40) cc_final: 0.7710 (m-40) REVERT: C 19 PHE cc_start: 0.8739 (m-80) cc_final: 0.8524 (m-80) REVERT: C 38 MET cc_start: 0.8775 (tmm) cc_final: 0.8426 (tmm) REVERT: C 39 CYS cc_start: 0.9237 (p) cc_final: 0.8893 (p) REVERT: C 60 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8477 (mt-10) REVERT: C 70 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8538 (mm-30) REVERT: C 92 ASP cc_start: 0.7993 (p0) cc_final: 0.7185 (p0) REVERT: C 105 ASP cc_start: 0.9384 (m-30) cc_final: 0.9116 (m-30) REVERT: D 44 ARG cc_start: 0.8827 (ptm160) cc_final: 0.8473 (ptm160) REVERT: D 60 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8893 (mm-30) REVERT: D 70 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8366 (mm-30) REVERT: D 90 VAL cc_start: 0.8785 (t) cc_final: 0.8572 (m) REVERT: D 92 ASP cc_start: 0.8860 (p0) cc_final: 0.8629 (p0) REVERT: D 116 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8262 (tpp80) REVERT: E 46 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8708 (tm-30) REVERT: E 49 PHE cc_start: 0.9671 (t80) cc_final: 0.9308 (t80) REVERT: E 75 ASP cc_start: 0.8673 (t0) cc_final: 0.8449 (t0) REVERT: E 92 ASP cc_start: 0.8027 (p0) cc_final: 0.7805 (p0) REVERT: E 105 ASP cc_start: 0.9238 (m-30) cc_final: 0.9036 (m-30) REVERT: E 112 LYS cc_start: 0.9424 (mtpp) cc_final: 0.9169 (mtmm) REVERT: F 38 MET cc_start: 0.8825 (tmm) cc_final: 0.8588 (tmm) REVERT: F 39 CYS cc_start: 0.9194 (p) cc_final: 0.8916 (p) REVERT: F 60 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8537 (mt-10) REVERT: F 70 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8476 (mm-30) REVERT: F 105 ASP cc_start: 0.9375 (m-30) cc_final: 0.9165 (m-30) REVERT: F 110 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8190 (mm-30) REVERT: F 127 TYR cc_start: 0.8822 (m-80) cc_final: 0.8598 (m-80) REVERT: G 70 GLU cc_start: 0.8656 (mm-30) cc_final: 0.7954 (tp30) REVERT: G 73 ARG cc_start: 0.9044 (ttp-170) cc_final: 0.8562 (ttp80) REVERT: G 92 ASP cc_start: 0.8508 (p0) cc_final: 0.8255 (p0) REVERT: G 110 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8981 (mm-30) REVERT: G 132 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: H 21 ASP cc_start: 0.7370 (p0) cc_final: 0.6849 (p0) REVERT: H 44 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8311 (ptm160) REVERT: H 46 GLN cc_start: 0.7734 (mt0) cc_final: 0.7480 (mt0) REVERT: H 89 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8509 (ttmm) REVERT: H 92 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7506 (p0) REVERT: H 98 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.9043 (p0) REVERT: H 105 ASP cc_start: 0.9085 (m-30) cc_final: 0.8869 (m-30) REVERT: H 119 LYS cc_start: 0.9541 (mmtm) cc_final: 0.9315 (mmtm) REVERT: H 124 ASP cc_start: 0.8890 (t0) cc_final: 0.8448 (t0) REVERT: I 13 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8663 (mt-10) REVERT: I 17 ASN cc_start: 0.9568 (m-40) cc_final: 0.9277 (m-40) REVERT: I 38 MET cc_start: 0.9004 (tmm) cc_final: 0.8792 (tmm) REVERT: I 39 CYS cc_start: 0.9202 (p) cc_final: 0.8694 (p) REVERT: I 60 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8556 (mt-10) REVERT: I 86 GLN cc_start: 0.8774 (tp40) cc_final: 0.8572 (tp40) REVERT: I 89 LYS cc_start: 0.9510 (ttpp) cc_final: 0.9173 (ttpp) REVERT: I 91 GLU cc_start: 0.8433 (pp20) cc_final: 0.8224 (pp20) REVERT: I 102 ASP cc_start: 0.8906 (m-30) cc_final: 0.8704 (m-30) REVERT: I 106 GLU cc_start: 0.9187 (tp30) cc_final: 0.8918 (mm-30) REVERT: J 13 GLU cc_start: 0.8526 (tp30) cc_final: 0.7988 (tp30) REVERT: J 17 ASN cc_start: 0.8556 (m110) cc_final: 0.7664 (m110) REVERT: J 21 ASP cc_start: 0.8411 (p0) cc_final: 0.8091 (p0) REVERT: J 25 THR cc_start: 0.8213 (p) cc_final: 0.7631 (t) REVERT: J 27 GLU cc_start: 0.7183 (mp0) cc_final: 0.6982 (mp0) REVERT: J 44 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8229 (mtp180) REVERT: J 76 LYS cc_start: 0.9422 (tttt) cc_final: 0.9002 (ptmm) REVERT: J 79 LYS cc_start: 0.8971 (mtmm) cc_final: 0.8656 (mtmm) REVERT: J 80 GLU cc_start: 0.8683 (mt-10) cc_final: 0.7887 (mt-10) REVERT: J 83 GLU cc_start: 0.7878 (pp20) cc_final: 0.7651 (tm-30) REVERT: J 110 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8450 (mm-30) REVERT: K 42 PHE cc_start: 0.9493 (m-80) cc_final: 0.8899 (m-10) REVERT: K 69 LYS cc_start: 0.9737 (tttp) cc_final: 0.9489 (ttmm) REVERT: K 89 LYS cc_start: 0.9221 (ptmm) cc_final: 0.8898 (ptmm) REVERT: K 116 ARG cc_start: 0.9215 (mmt-90) cc_final: 0.8856 (tpp80) REVERT: L 17 ASN cc_start: 0.9408 (m110) cc_final: 0.9145 (m-40) REVERT: L 21 ASP cc_start: 0.7552 (p0) cc_final: 0.7249 (p0) REVERT: L 38 MET cc_start: 0.8921 (tmm) cc_final: 0.8656 (tmm) REVERT: L 39 CYS cc_start: 0.9163 (p) cc_final: 0.8627 (p) REVERT: L 75 ASP cc_start: 0.8838 (t0) cc_final: 0.8089 (t0) REVERT: L 83 GLU cc_start: 0.8295 (mp0) cc_final: 0.7988 (mp0) REVERT: L 86 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8847 (tp40) REVERT: M 46 GLN cc_start: 0.6758 (tm-30) cc_final: 0.6084 (tm-30) REVERT: M 79 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8696 (mtmm) REVERT: M 83 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7522 (pp20) REVERT: M 102 ASP cc_start: 0.9269 (m-30) cc_final: 0.8813 (m-30) REVERT: M 106 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8552 (mp0) REVERT: M 116 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8545 (tpp80) REVERT: M 131 ASP cc_start: 0.8670 (t0) cc_final: 0.8406 (t0) REVERT: N 13 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8741 (mt-10) REVERT: N 15 TYR cc_start: 0.9238 (t80) cc_final: 0.8861 (t80) REVERT: N 31 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9255 (tp) REVERT: N 60 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8759 (mt-10) REVERT: N 90 VAL cc_start: 0.9050 (m) cc_final: 0.8637 (p) REVERT: N 92 ASP cc_start: 0.8102 (p0) cc_final: 0.7332 (p0) REVERT: N 97 MET cc_start: 0.9036 (mmm) cc_final: 0.8722 (mmm) REVERT: N 106 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8979 (mm-30) REVERT: O 13 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8807 (mt-10) REVERT: O 21 ASP cc_start: 0.7627 (p0) cc_final: 0.7178 (p0) REVERT: O 35 PHE cc_start: 0.9569 (t80) cc_final: 0.9091 (t80) REVERT: O 38 MET cc_start: 0.8752 (tmm) cc_final: 0.8540 (tmm) REVERT: O 39 CYS cc_start: 0.9127 (p) cc_final: 0.8837 (p) REVERT: O 86 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8897 (tp40) REVERT: O 91 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: O 94 THR cc_start: 0.9041 (m) cc_final: 0.8631 (p) REVERT: O 129 SER cc_start: 0.8887 (p) cc_final: 0.8454 (p) REVERT: O 131 ASP cc_start: 0.9206 (p0) cc_final: 0.8946 (m-30) REVERT: a 48 ASN cc_start: 0.9200 (t0) cc_final: 0.8666 (t0) REVERT: a 50 GLU cc_start: 0.8171 (mp0) cc_final: 0.7598 (mp0) REVERT: a 68 LEU cc_start: 0.9662 (tt) cc_final: 0.9278 (tt) REVERT: a 113 ASP cc_start: 0.9117 (t70) cc_final: 0.8893 (t0) REVERT: a 117 ASP cc_start: 0.9346 (m-30) cc_final: 0.9115 (m-30) REVERT: b 1 MET cc_start: 0.7389 (tpt) cc_final: 0.6105 (tpt) REVERT: b 91 VAL cc_start: 0.9424 (t) cc_final: 0.9184 (p) REVERT: c 5 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7126 (mtmm) REVERT: c 82 ASP cc_start: 0.7437 (t0) cc_final: 0.7196 (t0) REVERT: d 17 ILE cc_start: 0.8816 (pt) cc_final: 0.8607 (mm) REVERT: d 29 THR cc_start: 0.8609 (m) cc_final: 0.8235 (p) REVERT: d 82 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8469 (m-30) REVERT: e 30 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.7357 (p90) REVERT: e 108 LEU cc_start: 0.9015 (mt) cc_final: 0.8770 (mt) REVERT: f 5 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7713 (mtmm) REVERT: f 17 ILE cc_start: 0.7978 (mp) cc_final: 0.7601 (mm) REVERT: f 27 ASN cc_start: 0.8471 (m-40) cc_final: 0.7966 (m-40) REVERT: f 91 VAL cc_start: 0.9553 (t) cc_final: 0.9266 (m) REVERT: f 109 ASN cc_start: 0.8622 (m110) cc_final: 0.8151 (m-40) REVERT: g 48 ASN cc_start: 0.9142 (t0) cc_final: 0.8663 (t0) REVERT: g 50 GLU cc_start: 0.8137 (mp0) cc_final: 0.7662 (mp0) REVERT: g 68 LEU cc_start: 0.9453 (tt) cc_final: 0.9251 (tt) REVERT: g 91 VAL cc_start: 0.8724 (m) cc_final: 0.8487 (p) REVERT: h 1 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.4986 (ttp) REVERT: h 21 LEU cc_start: 0.9546 (mt) cc_final: 0.9294 (mt) REVERT: h 36 TYR cc_start: 0.8672 (m-80) cc_final: 0.8072 (m-10) REVERT: j 1 MET cc_start: 0.6585 (mtt) cc_final: 0.6362 (ttt) REVERT: j 48 ASN cc_start: 0.9056 (t0) cc_final: 0.8752 (t0) REVERT: j 50 GLU cc_start: 0.8126 (pm20) cc_final: 0.7453 (pm20) REVERT: k 58 ASN cc_start: 0.6585 (OUTLIER) cc_final: 0.6108 (m-40) REVERT: l 110 TYR cc_start: 0.8968 (t80) cc_final: 0.8742 (t80) REVERT: m 48 ASN cc_start: 0.8769 (t0) cc_final: 0.8486 (t0) REVERT: n 42 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.8216 (t70) REVERT: n 62 ASP cc_start: 0.9181 (t70) cc_final: 0.8870 (t0) REVERT: n 111 LEU cc_start: 0.9428 (mm) cc_final: 0.8994 (pp) outliers start: 238 outliers final: 147 residues processed: 1265 average time/residue: 0.4367 time to fit residues: 853.6827 Evaluate side-chains 1167 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1007 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 13 ASP Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 ASP Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 31 ASN Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 82 ASP Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 82 ASP Chi-restraints excluded: chain j residue 94 GLU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 58 ASN Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 30 PHE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 103 GLU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 9 ARG Chi-restraints excluded: chain o residue 13 ASP Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 106 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 341 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 273 optimal weight: 0.6980 overall best weight: 6.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 HIS ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 140 ASN ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN a 73 ASN ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN ** f 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 109 ASN ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 31470 Z= 0.370 Angle : 0.769 11.604 42780 Z= 0.409 Chirality : 0.046 0.183 4995 Planarity : 0.005 0.077 5565 Dihedral : 8.325 88.517 4312 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.30 % Favored : 90.57 % Rotamer: Outliers : 7.72 % Allowed : 21.19 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3795 helix: 0.42 (0.12), residues: 1666 sheet: -1.12 (0.20), residues: 590 loop : -2.47 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP o 16 HIS 0.018 0.002 HIS b 42 PHE 0.031 0.002 PHE M 49 TYR 0.032 0.002 TYR h 110 ARG 0.011 0.001 ARG l 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1079 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8485 (tp30) cc_final: 0.8070 (tp30) REVERT: A 17 ASN cc_start: 0.8711 (m110) cc_final: 0.8120 (m110) REVERT: A 38 MET cc_start: 0.9203 (tmm) cc_final: 0.8550 (tmm) REVERT: A 39 CYS cc_start: 0.8886 (p) cc_final: 0.8641 (p) REVERT: A 70 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8697 (tp30) REVERT: A 92 ASP cc_start: 0.8595 (p0) cc_final: 0.8371 (p0) REVERT: A 106 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 122 VAL cc_start: 0.9269 (t) cc_final: 0.9051 (p) REVERT: B 49 PHE cc_start: 0.9739 (t80) cc_final: 0.9422 (t80) REVERT: B 51 ASN cc_start: 0.9251 (m110) cc_final: 0.8983 (p0) REVERT: B 86 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8772 (tp-100) REVERT: C 13 GLU cc_start: 0.8676 (tp30) cc_final: 0.7708 (tp30) REVERT: C 17 ASN cc_start: 0.9305 (m-40) cc_final: 0.8288 (m-40) REVERT: C 19 PHE cc_start: 0.8752 (m-80) cc_final: 0.8524 (m-80) REVERT: C 38 MET cc_start: 0.8933 (tmm) cc_final: 0.8592 (tmm) REVERT: C 39 CYS cc_start: 0.9229 (p) cc_final: 0.8821 (p) REVERT: C 46 GLN cc_start: 0.8952 (pt0) cc_final: 0.8584 (pt0) REVERT: C 70 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8582 (mm-30) REVERT: C 86 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8572 (tp40) REVERT: C 105 ASP cc_start: 0.9379 (m-30) cc_final: 0.9137 (m-30) REVERT: C 124 ASP cc_start: 0.7373 (t0) cc_final: 0.6934 (t0) REVERT: D 44 ARG cc_start: 0.8774 (ptm160) cc_final: 0.8365 (ptm160) REVERT: D 60 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8955 (mm-30) REVERT: D 92 ASP cc_start: 0.9147 (p0) cc_final: 0.8828 (p0) REVERT: D 113 LYS cc_start: 0.9541 (mtpt) cc_final: 0.9262 (mtmt) REVERT: D 116 ARG cc_start: 0.8475 (tpp80) cc_final: 0.8087 (tpp80) REVERT: E 38 MET cc_start: 0.9069 (ttm) cc_final: 0.8860 (ttm) REVERT: E 46 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8880 (tm-30) REVERT: E 49 PHE cc_start: 0.9725 (t80) cc_final: 0.9450 (t80) REVERT: E 75 ASP cc_start: 0.8623 (t0) cc_final: 0.8365 (t0) REVERT: F 70 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8396 (mm-30) REVERT: F 86 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8560 (tp40) REVERT: F 105 ASP cc_start: 0.9375 (m-30) cc_final: 0.9161 (m-30) REVERT: F 110 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8211 (mm-30) REVERT: G 70 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8041 (tp30) REVERT: G 79 LYS cc_start: 0.9540 (mppt) cc_final: 0.9195 (mtmm) REVERT: G 92 ASP cc_start: 0.8701 (p0) cc_final: 0.8393 (p0) REVERT: G 113 LYS cc_start: 0.9429 (mttt) cc_final: 0.9158 (mtmt) REVERT: H 21 ASP cc_start: 0.7656 (p0) cc_final: 0.7076 (p0) REVERT: H 31 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9099 (tp) REVERT: H 44 ARG cc_start: 0.8810 (ptm-80) cc_final: 0.8120 (ttt180) REVERT: H 92 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7718 (p0) REVERT: H 98 ASN cc_start: 0.9323 (OUTLIER) cc_final: 0.8995 (p0) REVERT: H 105 ASP cc_start: 0.9100 (m-30) cc_final: 0.8885 (m-30) REVERT: H 119 LYS cc_start: 0.9529 (mmtm) cc_final: 0.9266 (mmtm) REVERT: H 124 ASP cc_start: 0.8951 (t0) cc_final: 0.8679 (t0) REVERT: I 13 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8669 (mt-10) REVERT: I 17 ASN cc_start: 0.9559 (m-40) cc_final: 0.9267 (m-40) REVERT: I 21 ASP cc_start: 0.8304 (p0) cc_final: 0.7995 (p0) REVERT: I 38 MET cc_start: 0.9112 (tmm) cc_final: 0.8759 (tmm) REVERT: I 39 CYS cc_start: 0.9140 (p) cc_final: 0.8724 (p) REVERT: I 60 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8423 (mt-10) REVERT: I 91 GLU cc_start: 0.8511 (pp20) cc_final: 0.8090 (pp20) REVERT: I 106 GLU cc_start: 0.9186 (tp30) cc_final: 0.8968 (mm-30) REVERT: I 116 ARG cc_start: 0.8501 (mmm160) cc_final: 0.8098 (mmm160) REVERT: J 13 GLU cc_start: 0.8465 (tp30) cc_final: 0.7924 (tp30) REVERT: J 17 ASN cc_start: 0.8536 (m110) cc_final: 0.7774 (m110) REVERT: J 21 ASP cc_start: 0.8475 (p0) cc_final: 0.8249 (p0) REVERT: J 83 GLU cc_start: 0.7931 (pp20) cc_final: 0.7575 (tm-30) REVERT: J 92 ASP cc_start: 0.9102 (p0) cc_final: 0.8885 (p0) REVERT: J 106 GLU cc_start: 0.9122 (tp30) cc_final: 0.8912 (mm-30) REVERT: J 112 LYS cc_start: 0.9469 (mtmm) cc_final: 0.9157 (mttp) REVERT: K 47 ASN cc_start: 0.9239 (p0) cc_final: 0.8924 (p0) REVERT: K 51 ASN cc_start: 0.9262 (m110) cc_final: 0.9003 (p0) REVERT: K 69 LYS cc_start: 0.9743 (tttp) cc_final: 0.9468 (ttmm) REVERT: K 86 GLN cc_start: 0.9019 (tp40) cc_final: 0.8688 (tp-100) REVERT: K 116 ARG cc_start: 0.9232 (mmt-90) cc_final: 0.8865 (mmt-90) REVERT: L 17 ASN cc_start: 0.9509 (m110) cc_final: 0.9265 (m-40) REVERT: L 21 ASP cc_start: 0.7819 (p0) cc_final: 0.7438 (p0) REVERT: L 26 SER cc_start: 0.8180 (t) cc_final: 0.7716 (p) REVERT: L 38 MET cc_start: 0.9018 (tmm) cc_final: 0.8797 (tmm) REVERT: L 39 CYS cc_start: 0.9187 (p) cc_final: 0.8613 (p) REVERT: L 46 GLN cc_start: 0.8855 (mt0) cc_final: 0.8587 (mt0) REVERT: L 83 GLU cc_start: 0.8206 (mp0) cc_final: 0.7948 (mp0) REVERT: L 86 GLN cc_start: 0.9347 (mm-40) cc_final: 0.8864 (tp40) REVERT: L 124 ASP cc_start: 0.8507 (t0) cc_final: 0.7778 (t0) REVERT: M 34 GLU cc_start: 0.8790 (tt0) cc_final: 0.8493 (tt0) REVERT: M 70 GLU cc_start: 0.9011 (tp30) cc_final: 0.8089 (tp30) REVERT: M 79 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8640 (mtmm) REVERT: M 83 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7549 (pp20) REVERT: M 102 ASP cc_start: 0.9200 (m-30) cc_final: 0.8973 (m-30) REVERT: M 106 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8543 (mp0) REVERT: M 116 ARG cc_start: 0.8796 (tpp80) cc_final: 0.8458 (tpp80) REVERT: M 131 ASP cc_start: 0.8749 (t0) cc_final: 0.8441 (t0) REVERT: N 59 ILE cc_start: 0.9792 (OUTLIER) cc_final: 0.9547 (mp) REVERT: N 90 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8199 (m) REVERT: N 92 ASP cc_start: 0.7920 (p0) cc_final: 0.7242 (p0) REVERT: N 98 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8761 (p0) REVERT: N 124 ASP cc_start: 0.8917 (t0) cc_final: 0.8137 (t0) REVERT: O 13 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8906 (mt-10) REVERT: O 15 TYR cc_start: 0.8828 (t80) cc_final: 0.8401 (t80) REVERT: O 21 ASP cc_start: 0.7682 (p0) cc_final: 0.7124 (p0) REVERT: O 39 CYS cc_start: 0.9112 (p) cc_final: 0.8771 (p) REVERT: O 60 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8357 (mt-10) REVERT: O 70 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8701 (mt-10) REVERT: O 86 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8852 (tp40) REVERT: O 94 THR cc_start: 0.9104 (m) cc_final: 0.8777 (p) REVERT: O 97 MET cc_start: 0.8994 (mmm) cc_final: 0.8757 (mmm) REVERT: a 48 ASN cc_start: 0.9154 (t0) cc_final: 0.8529 (t0) REVERT: a 50 GLU cc_start: 0.8100 (mp0) cc_final: 0.7507 (mp0) REVERT: a 112 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.8703 (mm-30) REVERT: a 113 ASP cc_start: 0.9151 (t70) cc_final: 0.8808 (t0) REVERT: a 117 ASP cc_start: 0.9438 (m-30) cc_final: 0.9175 (m-30) REVERT: b 1 MET cc_start: 0.7405 (tpt) cc_final: 0.6420 (tpt) REVERT: b 55 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8456 (t) REVERT: b 91 VAL cc_start: 0.9500 (t) cc_final: 0.9254 (p) REVERT: c 114 TYR cc_start: 0.8992 (t80) cc_final: 0.8751 (t80) REVERT: d 17 ILE cc_start: 0.9107 (pt) cc_final: 0.8880 (mm) REVERT: d 23 LEU cc_start: 0.9504 (tp) cc_final: 0.9255 (mm) REVERT: d 29 THR cc_start: 0.8896 (m) cc_final: 0.8519 (p) REVERT: e 5 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8131 (mtmm) REVERT: e 30 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7175 (p90) REVERT: e 103 GLU cc_start: -0.2041 (OUTLIER) cc_final: -0.3193 (pt0) REVERT: f 5 LYS cc_start: 0.8466 (mtmm) cc_final: 0.7644 (ptpp) REVERT: f 17 ILE cc_start: 0.8730 (mp) cc_final: 0.8301 (mm) REVERT: f 27 ASN cc_start: 0.8737 (m-40) cc_final: 0.8425 (m-40) REVERT: f 48 ASN cc_start: 0.9187 (m-40) cc_final: 0.8522 (m-40) REVERT: f 91 VAL cc_start: 0.9658 (t) cc_final: 0.9429 (m) REVERT: f 109 ASN cc_start: 0.8585 (m110) cc_final: 0.8337 (m110) REVERT: f 110 TYR cc_start: 0.9162 (t80) cc_final: 0.8822 (t80) REVERT: f 113 ASP cc_start: 0.9085 (m-30) cc_final: 0.8480 (p0) REVERT: g 1 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7051 (tmm) REVERT: g 14 GLN cc_start: 0.9008 (mp10) cc_final: 0.8756 (mm-40) REVERT: g 18 ASN cc_start: 0.9255 (p0) cc_final: 0.8969 (p0) REVERT: g 48 ASN cc_start: 0.9205 (t0) cc_final: 0.8674 (t0) REVERT: g 50 GLU cc_start: 0.8117 (mp0) cc_final: 0.7597 (mp0) REVERT: h 1 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.5147 (ttp) REVERT: h 21 LEU cc_start: 0.9562 (mt) cc_final: 0.9356 (mt) REVERT: h 36 TYR cc_start: 0.8792 (m-80) cc_final: 0.8206 (m-10) REVERT: i 53 PHE cc_start: 0.8819 (m-10) cc_final: 0.7841 (m-80) REVERT: j 48 ASN cc_start: 0.8918 (t0) cc_final: 0.8597 (t0) REVERT: j 50 GLU cc_start: 0.8262 (pm20) cc_final: 0.7379 (pm20) REVERT: k 5 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8167 (mtmm) REVERT: l 14 GLN cc_start: 0.8991 (mp10) cc_final: 0.8714 (mp10) REVERT: m 29 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7421 (p) REVERT: m 48 ASN cc_start: 0.8937 (t0) cc_final: 0.8532 (t0) REVERT: m 50 GLU cc_start: 0.8243 (mp0) cc_final: 0.7323 (mp0) REVERT: m 54 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.6908 (p0) REVERT: n 111 LEU cc_start: 0.9453 (mm) cc_final: 0.9082 (pp) REVERT: o 1 MET cc_start: 0.7548 (ttm) cc_final: 0.7252 (ttp) REVERT: o 54 ASN cc_start: 0.7674 (p0) cc_final: 0.6934 (p0) REVERT: o 65 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.5577 (t80) REVERT: o 77 SER cc_start: 0.9486 (p) cc_final: 0.9018 (p) outliers start: 272 outliers final: 172 residues processed: 1245 average time/residue: 0.4438 time to fit residues: 854.8906 Evaluate side-chains 1193 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1002 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 130 TYR Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 89 LYS Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain N residue 140 ASN Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 ASP Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 70 THR Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 86 ASP Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 121 ASN Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 94 GLU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 17 ILE Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 121 ASN Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 30 PHE Chi-restraints excluded: chain m residue 31 ASN Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 103 GLU Chi-restraints excluded: chain n residue 104 TYR Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 13 ASP Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 106 ASN Chi-restraints excluded: chain o residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 342 optimal weight: 9.9990 chunk 362 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 324 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 140 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 ASN L 17 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 140 ASN O 78 ASN a 10 HIS a 58 ASN ** b 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31470 Z= 0.349 Angle : 0.780 10.152 42780 Z= 0.412 Chirality : 0.046 0.223 4995 Planarity : 0.005 0.069 5565 Dihedral : 8.083 83.299 4290 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.46 % Favored : 90.41 % Rotamer: Outliers : 8.23 % Allowed : 23.35 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3795 helix: 0.39 (0.12), residues: 1663 sheet: -0.87 (0.20), residues: 612 loop : -2.48 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP o 16 HIS 0.012 0.001 HIS b 42 PHE 0.035 0.002 PHE J 49 TYR 0.034 0.002 TYR h 110 ARG 0.008 0.001 ARG g 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1071 time to evaluate : 4.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8424 (tp30) cc_final: 0.7998 (tp30) REVERT: A 17 ASN cc_start: 0.8706 (m110) cc_final: 0.8120 (m110) REVERT: A 38 MET cc_start: 0.9221 (tmm) cc_final: 0.8581 (tmm) REVERT: A 53 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8914 (mt) REVERT: A 70 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8656 (tp30) REVERT: A 106 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8563 (mt-10) REVERT: A 112 LYS cc_start: 0.9346 (mtmm) cc_final: 0.9066 (mtmm) REVERT: A 122 VAL cc_start: 0.9533 (t) cc_final: 0.8927 (p) REVERT: A 132 ASP cc_start: 0.8722 (m-30) cc_final: 0.7992 (t70) REVERT: B 49 PHE cc_start: 0.9726 (t80) cc_final: 0.9487 (t80) REVERT: B 86 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8839 (tp-100) REVERT: B 105 ASP cc_start: 0.9055 (m-30) cc_final: 0.8653 (p0) REVERT: B 131 ASP cc_start: 0.8994 (t0) cc_final: 0.8523 (t0) REVERT: C 13 GLU cc_start: 0.8677 (tp30) cc_final: 0.7759 (tp30) REVERT: C 17 ASN cc_start: 0.9315 (m-40) cc_final: 0.8363 (m-40) REVERT: C 38 MET cc_start: 0.8999 (tmm) cc_final: 0.8632 (tmm) REVERT: C 39 CYS cc_start: 0.9220 (p) cc_final: 0.8842 (p) REVERT: C 46 GLN cc_start: 0.8971 (pt0) cc_final: 0.8641 (pt0) REVERT: C 86 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8582 (tp40) REVERT: C 92 ASP cc_start: 0.8385 (p0) cc_final: 0.7659 (p0) REVERT: C 105 ASP cc_start: 0.9371 (m-30) cc_final: 0.9126 (m-30) REVERT: C 116 ARG cc_start: 0.8245 (mmm160) cc_final: 0.8045 (mmm160) REVERT: D 44 ARG cc_start: 0.8694 (ptm160) cc_final: 0.8257 (ptm160) REVERT: D 60 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8799 (mm-30) REVERT: D 70 GLU cc_start: 0.8321 (tp30) cc_final: 0.7825 (tp30) REVERT: D 76 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8104 (mmtm) REVERT: D 92 ASP cc_start: 0.9133 (p0) cc_final: 0.8728 (p0) REVERT: D 113 LYS cc_start: 0.9524 (mtpt) cc_final: 0.9257 (mtmt) REVERT: D 116 ARG cc_start: 0.8526 (tpp80) cc_final: 0.8253 (tpp80) REVERT: E 38 MET cc_start: 0.9008 (ttm) cc_final: 0.8792 (ttm) REVERT: E 46 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8913 (tm-30) REVERT: E 49 PHE cc_start: 0.9733 (t80) cc_final: 0.9455 (t80) REVERT: E 92 ASP cc_start: 0.8107 (p0) cc_final: 0.7872 (p0) REVERT: E 131 ASP cc_start: 0.8914 (m-30) cc_final: 0.8681 (m-30) REVERT: F 86 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8571 (tp40) REVERT: F 110 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8144 (mm-30) REVERT: G 34 GLU cc_start: 0.8415 (tt0) cc_final: 0.8051 (tt0) REVERT: G 70 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8128 (mm-30) REVERT: G 92 ASP cc_start: 0.8781 (p0) cc_final: 0.8549 (p0) REVERT: G 113 LYS cc_start: 0.9428 (mttt) cc_final: 0.9205 (mtmt) REVERT: G 116 ARG cc_start: 0.8915 (tpp80) cc_final: 0.8699 (tpp80) REVERT: G 132 ASP cc_start: 0.8536 (m-30) cc_final: 0.8174 (t70) REVERT: H 21 ASP cc_start: 0.7736 (p0) cc_final: 0.7169 (p0) REVERT: H 31 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9038 (tp) REVERT: H 44 ARG cc_start: 0.8966 (ptm-80) cc_final: 0.8486 (ttt180) REVERT: H 92 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7774 (p0) REVERT: H 98 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.8999 (p0) REVERT: H 105 ASP cc_start: 0.9099 (m-30) cc_final: 0.8872 (m-30) REVERT: H 119 LYS cc_start: 0.9538 (mmtm) cc_final: 0.9270 (mmtm) REVERT: H 124 ASP cc_start: 0.8861 (t0) cc_final: 0.8535 (t0) REVERT: I 13 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8641 (mt-10) REVERT: I 17 ASN cc_start: 0.9563 (m-40) cc_final: 0.9272 (m-40) REVERT: I 27 GLU cc_start: 0.7744 (mp0) cc_final: 0.7495 (pm20) REVERT: I 38 MET cc_start: 0.9106 (tmm) cc_final: 0.8751 (tmm) REVERT: I 39 CYS cc_start: 0.9118 (p) cc_final: 0.8771 (p) REVERT: I 60 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8555 (mt-10) REVERT: I 90 VAL cc_start: 0.9278 (t) cc_final: 0.9027 (t) REVERT: I 91 GLU cc_start: 0.8536 (pp20) cc_final: 0.8232 (pp20) REVERT: I 106 GLU cc_start: 0.9203 (tp30) cc_final: 0.8956 (mm-30) REVERT: I 116 ARG cc_start: 0.8538 (mmm160) cc_final: 0.8053 (mmm160) REVERT: I 119 LYS cc_start: 0.9227 (mmmt) cc_final: 0.9003 (mmmt) REVERT: I 124 ASP cc_start: 0.8532 (t0) cc_final: 0.7489 (t70) REVERT: J 13 GLU cc_start: 0.8488 (tp30) cc_final: 0.8085 (tp30) REVERT: J 21 ASP cc_start: 0.8492 (p0) cc_final: 0.8073 (p0) REVERT: J 70 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8340 (mm-30) REVERT: J 83 GLU cc_start: 0.7939 (pp20) cc_final: 0.7568 (tm-30) REVERT: J 110 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8457 (mm-30) REVERT: K 47 ASN cc_start: 0.9267 (p0) cc_final: 0.8962 (p0) REVERT: K 69 LYS cc_start: 0.9745 (tttp) cc_final: 0.9457 (ttmm) REVERT: K 75 ASP cc_start: 0.9074 (t0) cc_final: 0.8847 (t0) REVERT: K 86 GLN cc_start: 0.8976 (tp40) cc_final: 0.8646 (tp-100) REVERT: L 13 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8674 (mt-10) REVERT: L 17 ASN cc_start: 0.9544 (m-40) cc_final: 0.9245 (m-40) REVERT: L 38 MET cc_start: 0.9045 (tmm) cc_final: 0.8810 (tmm) REVERT: L 39 CYS cc_start: 0.9237 (p) cc_final: 0.8638 (p) REVERT: L 79 LYS cc_start: 0.9464 (mmtp) cc_final: 0.9158 (mmmm) REVERT: L 83 GLU cc_start: 0.8206 (mp0) cc_final: 0.7717 (mp0) REVERT: L 86 GLN cc_start: 0.9345 (mm-40) cc_final: 0.8979 (tp40) REVERT: L 124 ASP cc_start: 0.8488 (t0) cc_final: 0.7923 (t0) REVERT: M 17 ASN cc_start: 0.9428 (m-40) cc_final: 0.9211 (m110) REVERT: M 44 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.7911 (tpp80) REVERT: M 70 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: M 73 ARG cc_start: 0.9301 (tmm-80) cc_final: 0.8716 (ttp80) REVERT: M 83 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7462 (pp20) REVERT: M 86 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8455 (mm110) REVERT: M 102 ASP cc_start: 0.9183 (m-30) cc_final: 0.8947 (m-30) REVERT: M 106 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8541 (mp0) REVERT: M 116 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8438 (tpp80) REVERT: M 131 ASP cc_start: 0.8807 (t0) cc_final: 0.8464 (t0) REVERT: M 132 ASP cc_start: 0.8999 (m-30) cc_final: 0.8344 (m-30) REVERT: N 59 ILE cc_start: 0.9776 (OUTLIER) cc_final: 0.9553 (mp) REVERT: N 92 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7246 (p0) REVERT: N 98 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8711 (p0) REVERT: N 102 ASP cc_start: 0.8964 (m-30) cc_final: 0.8438 (m-30) REVERT: N 105 ASP cc_start: 0.9357 (m-30) cc_final: 0.9062 (p0) REVERT: N 124 ASP cc_start: 0.8509 (t0) cc_final: 0.7963 (t0) REVERT: O 13 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8898 (mt-10) REVERT: O 21 ASP cc_start: 0.7731 (p0) cc_final: 0.7089 (p0) REVERT: O 60 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8343 (mt-10) REVERT: O 86 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8789 (tp40) REVERT: O 97 MET cc_start: 0.9033 (mmm) cc_final: 0.8727 (mmm) REVERT: O 116 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7272 (mmm160) REVERT: O 119 LYS cc_start: 0.9282 (mmmt) cc_final: 0.9015 (mmmt) REVERT: a 48 ASN cc_start: 0.9146 (t0) cc_final: 0.8501 (t0) REVERT: a 50 GLU cc_start: 0.8126 (mp0) cc_final: 0.7612 (mp0) REVERT: a 112 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8638 (mm-30) REVERT: b 1 MET cc_start: 0.7821 (tpt) cc_final: 0.7089 (tpt) REVERT: b 55 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8624 (t) REVERT: b 91 VAL cc_start: 0.9496 (t) cc_final: 0.9243 (p) REVERT: c 58 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.6892 (p0) REVERT: c 114 TYR cc_start: 0.9086 (t80) cc_final: 0.8735 (t80) REVERT: d 29 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8381 (p) REVERT: d 97 ILE cc_start: 0.3278 (OUTLIER) cc_final: 0.2931 (mp) REVERT: e 30 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7216 (p90) REVERT: f 27 ASN cc_start: 0.8814 (m-40) cc_final: 0.8487 (m-40) REVERT: f 109 ASN cc_start: 0.8684 (m110) cc_final: 0.8398 (m110) REVERT: g 1 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6518 (tmm) REVERT: g 48 ASN cc_start: 0.9241 (t0) cc_final: 0.8689 (t0) REVERT: g 50 GLU cc_start: 0.8006 (mp0) cc_final: 0.7502 (mp0) REVERT: g 67 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9107 (mm) REVERT: h 1 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.5228 (ttp) REVERT: h 12 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8030 (p0) REVERT: h 36 TYR cc_start: 0.8713 (m-80) cc_final: 0.8320 (m-80) REVERT: i 1 MET cc_start: 0.7323 (ttm) cc_final: 0.6989 (ttm) REVERT: i 112 GLU cc_start: 0.9443 (mm-30) cc_final: 0.8969 (mm-30) REVERT: j 1 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5765 (ttt) REVERT: j 48 ASN cc_start: 0.9076 (t0) cc_final: 0.8670 (t0) REVERT: j 50 GLU cc_start: 0.8403 (pm20) cc_final: 0.7448 (pm20) REVERT: k 5 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8252 (mtmm) REVERT: k 67 ILE cc_start: 0.8135 (mp) cc_final: 0.7861 (mp) REVERT: m 2 ARG cc_start: 0.5373 (OUTLIER) cc_final: 0.4685 (mtt180) REVERT: m 13 ASP cc_start: 0.8190 (m-30) cc_final: 0.7985 (m-30) REVERT: m 29 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7718 (p) REVERT: m 48 ASN cc_start: 0.9089 (t0) cc_final: 0.8616 (t0) REVERT: m 50 GLU cc_start: 0.8305 (mp0) cc_final: 0.7309 (mp0) REVERT: n 98 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6704 (tp) REVERT: n 111 LEU cc_start: 0.9464 (mm) cc_final: 0.9108 (pp) REVERT: o 50 GLU cc_start: 0.7326 (tp30) cc_final: 0.6982 (tp30) REVERT: o 54 ASN cc_start: 0.8031 (p0) cc_final: 0.7357 (p0) REVERT: o 65 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.5812 (t80) REVERT: o 77 SER cc_start: 0.9467 (p) cc_final: 0.8969 (p) outliers start: 290 outliers final: 194 residues processed: 1256 average time/residue: 0.4501 time to fit residues: 870.2746 Evaluate side-chains 1215 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 997 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 130 TYR Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 81 SER Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 106 ASN Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 70 THR Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 86 ASP Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 3 ARG Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 106 ASN Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 94 GLU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 17 ILE Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain k residue 121 ASN Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 2 ARG Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 103 GLU Chi-restraints excluded: chain n residue 104 TYR Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 13 ASP Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 106 ASN Chi-restraints excluded: chain o residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 309 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 ASN E 51 ASN ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 31 ASN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 ASN ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 18 ASN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN l 58 ASN ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31470 Z= 0.240 Angle : 0.754 11.103 42780 Z= 0.391 Chirality : 0.045 0.189 4995 Planarity : 0.005 0.091 5565 Dihedral : 7.690 59.772 4279 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.99 % Favored : 90.91 % Rotamer: Outliers : 7.83 % Allowed : 24.96 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 3795 helix: 0.46 (0.12), residues: 1656 sheet: -0.64 (0.20), residues: 613 loop : -2.43 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 16 HIS 0.008 0.001 HIS b 42 PHE 0.026 0.002 PHE J 49 TYR 0.032 0.002 TYR m 110 ARG 0.010 0.001 ARG c 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1127 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8400 (tp30) cc_final: 0.7890 (tp30) REVERT: A 17 ASN cc_start: 0.8645 (m110) cc_final: 0.7954 (m110) REVERT: A 38 MET cc_start: 0.9165 (tmm) cc_final: 0.8408 (tmm) REVERT: A 53 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8916 (mt) REVERT: A 92 ASP cc_start: 0.8742 (p0) cc_final: 0.8387 (p0) REVERT: A 106 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8517 (mt-10) REVERT: A 112 LYS cc_start: 0.9406 (mtmm) cc_final: 0.9122 (mtmm) REVERT: A 122 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.8984 (p) REVERT: A 124 ASP cc_start: 0.9157 (t0) cc_final: 0.8912 (t0) REVERT: A 132 ASP cc_start: 0.8658 (m-30) cc_final: 0.7892 (t70) REVERT: B 49 PHE cc_start: 0.9715 (t80) cc_final: 0.9411 (t80) REVERT: B 86 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8756 (tp-100) REVERT: B 116 ARG cc_start: 0.9036 (tpp80) cc_final: 0.8762 (tpp80) REVERT: B 131 ASP cc_start: 0.8715 (t0) cc_final: 0.8454 (t0) REVERT: C 13 GLU cc_start: 0.8671 (tp30) cc_final: 0.7664 (tp30) REVERT: C 17 ASN cc_start: 0.9319 (m-40) cc_final: 0.8278 (m-40) REVERT: C 38 MET cc_start: 0.8970 (tmm) cc_final: 0.8556 (tmm) REVERT: C 39 CYS cc_start: 0.9184 (p) cc_final: 0.8787 (p) REVERT: C 46 GLN cc_start: 0.8900 (pt0) cc_final: 0.8676 (pt0) REVERT: C 60 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8449 (mt-10) REVERT: C 86 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8356 (tp40) REVERT: C 105 ASP cc_start: 0.9361 (m-30) cc_final: 0.9112 (m-30) REVERT: C 116 ARG cc_start: 0.8275 (mmm160) cc_final: 0.8057 (mmm160) REVERT: D 60 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8866 (mm-30) REVERT: D 69 LYS cc_start: 0.9627 (OUTLIER) cc_final: 0.9356 (ttpp) REVERT: D 112 LYS cc_start: 0.9428 (mtmm) cc_final: 0.9003 (mtmm) REVERT: D 116 ARG cc_start: 0.8351 (tpp80) cc_final: 0.8095 (tpp80) REVERT: D 132 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7480 (t0) REVERT: E 17 ASN cc_start: 0.9349 (m-40) cc_final: 0.9131 (m-40) REVERT: E 44 ARG cc_start: 0.8304 (tpt-90) cc_final: 0.8098 (tpt-90) REVERT: E 46 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8966 (tm-30) REVERT: E 49 PHE cc_start: 0.9737 (t80) cc_final: 0.9484 (t80) REVERT: F 60 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8615 (mt-10) REVERT: F 70 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8558 (mt-10) REVERT: F 86 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8493 (tp40) REVERT: F 97 MET cc_start: 0.8578 (mmm) cc_final: 0.8373 (mmt) REVERT: F 110 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8201 (mm-30) REVERT: G 29 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8341 (tm-30) REVERT: G 44 ARG cc_start: 0.8752 (ptm160) cc_final: 0.7819 (ttm-80) REVERT: G 46 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: G 70 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8022 (tp30) REVERT: G 75 ASP cc_start: 0.8825 (p0) cc_final: 0.8498 (p0) REVERT: G 92 ASP cc_start: 0.8757 (p0) cc_final: 0.8472 (p0) REVERT: G 113 LYS cc_start: 0.9393 (mttt) cc_final: 0.9103 (mtmt) REVERT: G 132 ASP cc_start: 0.8504 (m-30) cc_final: 0.8055 (t70) REVERT: H 21 ASP cc_start: 0.7806 (p0) cc_final: 0.7245 (p0) REVERT: H 31 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9030 (tp) REVERT: H 44 ARG cc_start: 0.9099 (ptm-80) cc_final: 0.8698 (ttt180) REVERT: H 92 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7753 (p0) REVERT: H 98 ASN cc_start: 0.9288 (OUTLIER) cc_final: 0.8967 (p0) REVERT: H 105 ASP cc_start: 0.9083 (m-30) cc_final: 0.8872 (m-30) REVERT: I 13 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8580 (mt-10) REVERT: I 17 ASN cc_start: 0.9551 (m-40) cc_final: 0.9223 (m-40) REVERT: I 38 MET cc_start: 0.9094 (tmm) cc_final: 0.8816 (tmm) REVERT: I 39 CYS cc_start: 0.9100 (p) cc_final: 0.8691 (p) REVERT: I 59 ILE cc_start: 0.9609 (OUTLIER) cc_final: 0.9387 (tp) REVERT: I 60 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8610 (mt-10) REVERT: I 99 TYR cc_start: 0.8609 (t80) cc_final: 0.8261 (t80) REVERT: I 106 GLU cc_start: 0.9187 (tp30) cc_final: 0.8961 (mm-30) REVERT: I 116 ARG cc_start: 0.8482 (mmm160) cc_final: 0.8035 (mmm160) REVERT: J 13 GLU cc_start: 0.8442 (tp30) cc_final: 0.8079 (tp30) REVERT: J 21 ASP cc_start: 0.8532 (p0) cc_final: 0.8126 (p0) REVERT: J 27 GLU cc_start: 0.6949 (mp0) cc_final: 0.6731 (mp0) REVERT: J 70 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8086 (tp30) REVERT: J 83 GLU cc_start: 0.7822 (pp20) cc_final: 0.7544 (tm-30) REVERT: K 47 ASN cc_start: 0.9194 (p0) cc_final: 0.8892 (p0) REVERT: K 69 LYS cc_start: 0.9739 (tttp) cc_final: 0.9448 (ttmm) REVERT: K 86 GLN cc_start: 0.8900 (tp40) cc_final: 0.8574 (tp-100) REVERT: K 112 LYS cc_start: 0.9465 (mtmm) cc_final: 0.9150 (mttp) REVERT: L 17 ASN cc_start: 0.9512 (m-40) cc_final: 0.9218 (m-40) REVERT: L 21 ASP cc_start: 0.7888 (p0) cc_final: 0.7502 (p0) REVERT: L 38 MET cc_start: 0.9048 (tmm) cc_final: 0.8805 (tmm) REVERT: L 39 CYS cc_start: 0.9209 (p) cc_final: 0.8609 (p) REVERT: L 46 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8774 (mm-40) REVERT: L 83 GLU cc_start: 0.8012 (mp0) cc_final: 0.7760 (mp0) REVERT: L 86 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8897 (tp40) REVERT: M 17 ASN cc_start: 0.9431 (m-40) cc_final: 0.9212 (m110) REVERT: M 70 GLU cc_start: 0.8984 (tp30) cc_final: 0.7937 (tp30) REVERT: M 83 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7462 (pp20) REVERT: M 86 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8396 (mm110) REVERT: M 106 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8511 (mp0) REVERT: M 131 ASP cc_start: 0.8802 (t0) cc_final: 0.8453 (t0) REVERT: M 132 ASP cc_start: 0.8962 (m-30) cc_final: 0.8225 (m-30) REVERT: N 75 ASP cc_start: 0.8948 (t0) cc_final: 0.8692 (t0) REVERT: N 90 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8739 (p) REVERT: N 92 ASP cc_start: 0.7992 (p0) cc_final: 0.7467 (p0) REVERT: N 98 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8642 (p0) REVERT: N 105 ASP cc_start: 0.9312 (m-30) cc_final: 0.9086 (m-30) REVERT: O 21 ASP cc_start: 0.7655 (p0) cc_final: 0.7267 (p0) REVERT: O 60 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8427 (mt-10) REVERT: O 94 THR cc_start: 0.9085 (m) cc_final: 0.8768 (p) REVERT: O 97 MET cc_start: 0.8972 (mmm) cc_final: 0.8723 (mmm) REVERT: O 99 TYR cc_start: 0.8462 (t80) cc_final: 0.8080 (t80) REVERT: O 110 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8468 (mm-30) REVERT: a 48 ASN cc_start: 0.9117 (t0) cc_final: 0.8477 (t0) REVERT: a 50 GLU cc_start: 0.8100 (mp0) cc_final: 0.7432 (mp0) REVERT: a 101 ASP cc_start: 0.9091 (p0) cc_final: 0.8887 (p0) REVERT: a 112 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.8773 (mm-30) REVERT: a 113 ASP cc_start: 0.9125 (t0) cc_final: 0.8853 (t0) REVERT: b 1 MET cc_start: 0.7816 (tpt) cc_final: 0.7122 (tpt) REVERT: b 18 ASN cc_start: 0.9160 (t0) cc_final: 0.8784 (t0) REVERT: b 55 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8649 (t) REVERT: b 91 VAL cc_start: 0.9478 (t) cc_final: 0.9222 (p) REVERT: c 3 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7127 (ttp80) REVERT: c 58 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.6806 (p0) REVERT: c 79 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7891 (t) REVERT: d 29 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8398 (p) REVERT: d 54 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8541 (m-40) REVERT: d 97 ILE cc_start: 0.4049 (OUTLIER) cc_final: 0.3815 (mt) REVERT: e 30 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.6848 (p90) REVERT: f 27 ASN cc_start: 0.8859 (m-40) cc_final: 0.8533 (m-40) REVERT: f 109 ASN cc_start: 0.8680 (m110) cc_final: 0.8408 (m110) REVERT: f 113 ASP cc_start: 0.9135 (m-30) cc_final: 0.8588 (p0) REVERT: g 67 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9046 (mp) REVERT: h 1 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.5144 (ttp) REVERT: h 14 GLN cc_start: 0.8780 (mp10) cc_final: 0.8393 (mp10) REVERT: h 36 TYR cc_start: 0.8687 (m-80) cc_final: 0.8381 (m-10) REVERT: j 12 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8019 (p0) REVERT: j 48 ASN cc_start: 0.9043 (t0) cc_final: 0.8616 (t0) REVERT: j 50 GLU cc_start: 0.8417 (pm20) cc_final: 0.7460 (pm20) REVERT: k 5 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8325 (mtmm) REVERT: m 13 ASP cc_start: 0.7948 (m-30) cc_final: 0.7731 (m-30) REVERT: m 29 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7564 (p) REVERT: m 48 ASN cc_start: 0.9069 (t0) cc_final: 0.8632 (t0) REVERT: m 50 GLU cc_start: 0.8349 (mp0) cc_final: 0.7397 (pm20) REVERT: m 54 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.6845 (p0) REVERT: n 36 TYR cc_start: 0.8537 (m-80) cc_final: 0.8331 (m-10) REVERT: n 107 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8490 (m) REVERT: n 111 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9116 (pp) REVERT: o 1 MET cc_start: 0.7575 (ttp) cc_final: 0.7303 (ttm) REVERT: o 50 GLU cc_start: 0.7351 (tp30) cc_final: 0.6980 (tp30) REVERT: o 54 ASN cc_start: 0.8000 (p0) cc_final: 0.7189 (p0) REVERT: o 65 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.5678 (t80) REVERT: o 77 SER cc_start: 0.9411 (p) cc_final: 0.8912 (p) outliers start: 276 outliers final: 175 residues processed: 1298 average time/residue: 0.4285 time to fit residues: 860.7399 Evaluate side-chains 1237 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1032 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 48 ASN Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 54 ASN Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 86 ASP Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 42 HIS Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 106 ASN Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 17 ILE Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 103 GLU Chi-restraints excluded: chain n residue 104 TYR Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 13 ASP Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 106 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 0.2980 chunk 190 optimal weight: 6.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN ** b 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 ASN ** f 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31470 Z= 0.327 Angle : 0.787 10.605 42780 Z= 0.413 Chirality : 0.046 0.212 4995 Planarity : 0.005 0.065 5565 Dihedral : 7.565 59.665 4266 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.72 % Favored : 90.17 % Rotamer: Outliers : 8.43 % Allowed : 25.79 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3795 helix: 0.32 (0.12), residues: 1656 sheet: -0.61 (0.21), residues: 617 loop : -2.43 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o 16 HIS 0.009 0.001 HIS b 42 PHE 0.036 0.002 PHE K 49 TYR 0.038 0.002 TYR m 110 ARG 0.011 0.001 ARG n 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1384 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1087 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8411 (tp30) cc_final: 0.7908 (tp30) REVERT: A 17 ASN cc_start: 0.8710 (m110) cc_final: 0.7952 (m110) REVERT: A 30 GLU cc_start: 0.8551 (pm20) cc_final: 0.8214 (pm20) REVERT: A 38 MET cc_start: 0.9184 (tmm) cc_final: 0.8676 (tmm) REVERT: A 53 LEU cc_start: 0.9350 (mm) cc_final: 0.8948 (mt) REVERT: A 70 GLU cc_start: 0.8786 (tp30) cc_final: 0.8232 (tp30) REVERT: A 92 ASP cc_start: 0.8893 (p0) cc_final: 0.8581 (p0) REVERT: A 106 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8526 (mt-10) REVERT: A 122 VAL cc_start: 0.9505 (OUTLIER) cc_final: 0.8922 (p) REVERT: A 132 ASP cc_start: 0.8774 (m-30) cc_final: 0.7962 (t70) REVERT: B 86 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8780 (tp-100) REVERT: B 105 ASP cc_start: 0.9086 (m-30) cc_final: 0.8577 (p0) REVERT: C 13 GLU cc_start: 0.8683 (tp30) cc_final: 0.7808 (tp30) REVERT: C 17 ASN cc_start: 0.9326 (m-40) cc_final: 0.8482 (m-40) REVERT: C 38 MET cc_start: 0.9015 (tmm) cc_final: 0.8599 (tmm) REVERT: C 39 CYS cc_start: 0.9128 (p) cc_final: 0.8784 (p) REVERT: C 46 GLN cc_start: 0.8922 (pt0) cc_final: 0.8687 (pt0) REVERT: C 86 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8359 (tp40) REVERT: C 90 VAL cc_start: 0.9364 (t) cc_final: 0.9043 (p) REVERT: C 92 ASP cc_start: 0.8375 (p0) cc_final: 0.7652 (p0) REVERT: C 105 ASP cc_start: 0.9377 (m-30) cc_final: 0.9132 (m-30) REVERT: D 21 ASP cc_start: 0.7417 (p0) cc_final: 0.7179 (p0) REVERT: D 44 ARG cc_start: 0.8724 (ptm160) cc_final: 0.8334 (ptm160) REVERT: D 60 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8801 (mm-30) REVERT: D 70 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8413 (mm-30) REVERT: D 75 ASP cc_start: 0.8632 (p0) cc_final: 0.8361 (p0) REVERT: D 83 GLU cc_start: 0.8075 (tt0) cc_final: 0.7705 (pt0) REVERT: D 92 ASP cc_start: 0.9143 (p0) cc_final: 0.8854 (p0) REVERT: D 106 GLU cc_start: 0.8783 (tp30) cc_final: 0.8367 (tp30) REVERT: D 132 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7603 (t0) REVERT: E 17 ASN cc_start: 0.9322 (m-40) cc_final: 0.8999 (m-40) REVERT: E 46 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.9076 (tm-30) REVERT: E 92 ASP cc_start: 0.7823 (p0) cc_final: 0.7564 (p0) REVERT: E 105 ASP cc_start: 0.9069 (m-30) cc_final: 0.8665 (p0) REVERT: F 70 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8567 (mt-10) REVERT: F 86 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8521 (tp40) REVERT: F 110 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8211 (mm-30) REVERT: G 21 ASP cc_start: 0.8155 (p0) cc_final: 0.7706 (p0) REVERT: G 29 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8331 (tm-30) REVERT: G 60 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8776 (mt-10) REVERT: G 70 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8020 (tp30) REVERT: G 92 ASP cc_start: 0.8815 (p0) cc_final: 0.8555 (p0) REVERT: G 132 ASP cc_start: 0.8630 (m-30) cc_final: 0.8171 (t70) REVERT: H 31 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9039 (tp) REVERT: H 44 ARG cc_start: 0.9083 (ptm-80) cc_final: 0.8389 (ttp80) REVERT: H 92 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7946 (p0) REVERT: H 98 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.8904 (p0) REVERT: H 105 ASP cc_start: 0.9086 (m-30) cc_final: 0.8858 (m-30) REVERT: H 116 ARG cc_start: 0.8801 (tpp80) cc_final: 0.8535 (tpp80) REVERT: I 17 ASN cc_start: 0.9549 (m-40) cc_final: 0.9265 (m-40) REVERT: I 38 MET cc_start: 0.9072 (tmm) cc_final: 0.8710 (tmm) REVERT: I 39 CYS cc_start: 0.9128 (p) cc_final: 0.8732 (p) REVERT: I 54 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9054 (pp) REVERT: I 56 LEU cc_start: 0.9263 (tt) cc_final: 0.8879 (mt) REVERT: I 59 ILE cc_start: 0.9606 (OUTLIER) cc_final: 0.9394 (tp) REVERT: I 60 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8672 (mt-10) REVERT: I 76 LYS cc_start: 0.9477 (mmmm) cc_final: 0.9254 (mmmm) REVERT: I 106 GLU cc_start: 0.9257 (tp30) cc_final: 0.8985 (mm-30) REVERT: I 116 ARG cc_start: 0.8534 (mmm160) cc_final: 0.8006 (mmm160) REVERT: I 119 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8960 (mmmt) REVERT: J 13 GLU cc_start: 0.8497 (tp30) cc_final: 0.8130 (tp30) REVERT: J 21 ASP cc_start: 0.8494 (p0) cc_final: 0.8072 (p0) REVERT: J 27 GLU cc_start: 0.7068 (mp0) cc_final: 0.6842 (mp0) REVERT: J 34 GLU cc_start: 0.8725 (tt0) cc_final: 0.8291 (tt0) REVERT: J 60 GLU cc_start: 0.8754 (mp0) cc_final: 0.8539 (mp0) REVERT: J 70 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8038 (tp30) REVERT: J 83 GLU cc_start: 0.7949 (pp20) cc_final: 0.7639 (tm-30) REVERT: J 92 ASP cc_start: 0.8985 (p0) cc_final: 0.8631 (p0) REVERT: J 112 LYS cc_start: 0.9386 (mtmm) cc_final: 0.9117 (mttm) REVERT: K 49 PHE cc_start: 0.9687 (t80) cc_final: 0.9423 (t80) REVERT: K 69 LYS cc_start: 0.9741 (tttp) cc_final: 0.9460 (ttmm) REVERT: K 86 GLN cc_start: 0.8908 (tp40) cc_final: 0.8551 (tp-100) REVERT: K 105 ASP cc_start: 0.9317 (m-30) cc_final: 0.8857 (p0) REVERT: K 112 LYS cc_start: 0.9515 (mtmm) cc_final: 0.9264 (mtmm) REVERT: L 17 ASN cc_start: 0.9562 (m-40) cc_final: 0.9256 (m-40) REVERT: L 21 ASP cc_start: 0.7991 (p0) cc_final: 0.7584 (p0) REVERT: L 38 MET cc_start: 0.9011 (tmm) cc_final: 0.8768 (tmm) REVERT: L 39 CYS cc_start: 0.9234 (p) cc_final: 0.8609 (p) REVERT: L 83 GLU cc_start: 0.8071 (mp0) cc_final: 0.7849 (mp0) REVERT: L 86 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8883 (tp40) REVERT: M 17 ASN cc_start: 0.9461 (m-40) cc_final: 0.9235 (m110) REVERT: M 83 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7495 (pp20) REVERT: M 86 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8374 (mm110) REVERT: M 106 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8553 (mp0) REVERT: M 116 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8561 (tpp80) REVERT: M 131 ASP cc_start: 0.8825 (t0) cc_final: 0.8473 (t0) REVERT: M 132 ASP cc_start: 0.8966 (m-30) cc_final: 0.8295 (m-30) REVERT: N 75 ASP cc_start: 0.8793 (t0) cc_final: 0.8440 (t0) REVERT: N 97 MET cc_start: 0.8991 (mmm) cc_final: 0.8743 (mmm) REVERT: N 98 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8829 (p0) REVERT: N 105 ASP cc_start: 0.9314 (m-30) cc_final: 0.9013 (m-30) REVERT: O 21 ASP cc_start: 0.7733 (p0) cc_final: 0.7295 (p0) REVERT: O 35 PHE cc_start: 0.9525 (t80) cc_final: 0.9321 (t80) REVERT: O 60 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8378 (mt-10) REVERT: O 94 THR cc_start: 0.9229 (m) cc_final: 0.8903 (p) REVERT: O 97 MET cc_start: 0.8983 (mmm) cc_final: 0.8683 (mmm) REVERT: O 110 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8570 (mm-30) REVERT: a 112 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8590 (mm-30) REVERT: b 1 MET cc_start: 0.8086 (tpt) cc_final: 0.7273 (tpt) REVERT: b 55 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8714 (t) REVERT: b 91 VAL cc_start: 0.9510 (t) cc_final: 0.9248 (p) REVERT: c 3 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7305 (ttp80) REVERT: c 58 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.6906 (p0) REVERT: c 79 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7927 (t) REVERT: c 114 TYR cc_start: 0.9027 (t80) cc_final: 0.8618 (t80) REVERT: d 13 ASP cc_start: 0.8570 (m-30) cc_final: 0.8326 (m-30) REVERT: d 29 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8534 (p) REVERT: d 54 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8549 (m-40) REVERT: d 97 ILE cc_start: 0.4396 (OUTLIER) cc_final: 0.4097 (mp) REVERT: e 30 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7185 (p90) REVERT: e 103 GLU cc_start: -0.1891 (OUTLIER) cc_final: -0.2607 (pt0) REVERT: f 3 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7887 (ttp-110) REVERT: f 27 ASN cc_start: 0.8816 (m-40) cc_final: 0.8420 (m-40) REVERT: f 109 ASN cc_start: 0.8756 (m110) cc_final: 0.8478 (m110) REVERT: g 48 ASN cc_start: 0.9193 (t0) cc_final: 0.8819 (t0) REVERT: g 86 ASP cc_start: 0.8620 (m-30) cc_final: 0.8303 (t0) REVERT: h 1 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.5434 (ttp) REVERT: h 12 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8040 (p0) REVERT: h 74 LYS cc_start: 0.9387 (mmtp) cc_final: 0.9173 (mmmm) REVERT: i 1 MET cc_start: 0.7412 (ttm) cc_final: 0.7198 (ttm) REVERT: j 1 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6271 (ttm) REVERT: j 12 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8108 (p0) REVERT: j 48 ASN cc_start: 0.9113 (t0) cc_final: 0.8777 (t0) REVERT: j 50 GLU cc_start: 0.8370 (pm20) cc_final: 0.7424 (pm20) REVERT: j 101 ASP cc_start: 0.8083 (p0) cc_final: 0.7761 (p0) REVERT: j 112 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8708 (tm-30) REVERT: k 5 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: k 75 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8804 (mmtt) REVERT: l 93 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8393 (tpt170) REVERT: m 2 ARG cc_start: 0.5449 (OUTLIER) cc_final: 0.5034 (mtp180) REVERT: m 13 ASP cc_start: 0.8123 (m-30) cc_final: 0.7877 (m-30) REVERT: m 29 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7937 (p) REVERT: m 48 ASN cc_start: 0.9156 (t0) cc_final: 0.8681 (t0) REVERT: m 54 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6754 (p0) REVERT: n 104 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: n 111 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9133 (pp) REVERT: o 1 MET cc_start: 0.7927 (ttp) cc_final: 0.7511 (tmm) REVERT: o 50 GLU cc_start: 0.7500 (tp30) cc_final: 0.7044 (tp30) REVERT: o 54 ASN cc_start: 0.8253 (p0) cc_final: 0.7801 (p0) REVERT: o 65 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6028 (t80) REVERT: o 77 SER cc_start: 0.9425 (p) cc_final: 0.8908 (p) outliers start: 297 outliers final: 212 residues processed: 1277 average time/residue: 0.4650 time to fit residues: 925.4740 Evaluate side-chains 1248 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1004 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 112 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain N residue 140 ASN Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 48 ASN Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 106 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 54 ASN Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 86 ASP Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 42 HIS Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 106 ASN Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 48 ASN Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 70 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 2 ARG Chi-restraints excluded: chain m residue 23 LEU Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 HIS Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 17 ILE Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 104 TYR Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 13 ASP Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 ARG Chi-restraints excluded: chain o residue 105 THR Chi-restraints excluded: chain o residue 106 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 chunk 202 optimal weight: 0.0870 chunk 361 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 ASN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN a 48 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 73 ASN ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 34 ASN ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31470 Z= 0.239 Angle : 0.795 15.672 42780 Z= 0.410 Chirality : 0.046 0.225 4995 Planarity : 0.005 0.065 5565 Dihedral : 7.437 59.266 4261 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.91 % Favored : 91.01 % Rotamer: Outliers : 7.32 % Allowed : 28.34 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3795 helix: 0.35 (0.12), residues: 1657 sheet: -0.41 (0.21), residues: 613 loop : -2.36 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP o 16 HIS 0.006 0.001 HIS b 42 PHE 0.052 0.002 PHE c 89 TYR 0.035 0.002 TYR m 110 ARG 0.010 0.001 ARG a 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1148 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8338 (tp30) cc_final: 0.7773 (tp30) REVERT: A 17 ASN cc_start: 0.8669 (m110) cc_final: 0.7858 (m110) REVERT: A 30 GLU cc_start: 0.8564 (pm20) cc_final: 0.8236 (pm20) REVERT: A 38 MET cc_start: 0.9193 (tmm) cc_final: 0.8640 (tmm) REVERT: A 53 LEU cc_start: 0.9350 (mm) cc_final: 0.9040 (mt) REVERT: A 92 ASP cc_start: 0.8847 (p0) cc_final: 0.8633 (p0) REVERT: A 122 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.8946 (p) REVERT: A 124 ASP cc_start: 0.9154 (t0) cc_final: 0.8867 (t0) REVERT: A 132 ASP cc_start: 0.8788 (m-30) cc_final: 0.7940 (t70) REVERT: B 116 ARG cc_start: 0.9046 (tpp80) cc_final: 0.8771 (tpp80) REVERT: B 131 ASP cc_start: 0.8902 (t0) cc_final: 0.8623 (t0) REVERT: C 13 GLU cc_start: 0.8642 (tp30) cc_final: 0.7616 (tp30) REVERT: C 17 ASN cc_start: 0.9328 (m-40) cc_final: 0.8230 (m-40) REVERT: C 38 MET cc_start: 0.8978 (tmm) cc_final: 0.8616 (tmm) REVERT: C 60 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8475 (mt-10) REVERT: C 86 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8250 (tp40) REVERT: C 105 ASP cc_start: 0.9356 (m-30) cc_final: 0.9105 (m-30) REVERT: D 15 TYR cc_start: 0.8879 (t80) cc_final: 0.8668 (t80) REVERT: D 21 ASP cc_start: 0.7364 (p0) cc_final: 0.7057 (p0) REVERT: D 44 ARG cc_start: 0.8728 (ptm160) cc_final: 0.8342 (ptm160) REVERT: D 60 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8823 (mm-30) REVERT: D 69 LYS cc_start: 0.9624 (OUTLIER) cc_final: 0.9348 (ttpp) REVERT: D 116 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8265 (tpp80) REVERT: D 132 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7451 (t0) REVERT: E 17 ASN cc_start: 0.9343 (m-40) cc_final: 0.9100 (m-40) REVERT: E 21 ASP cc_start: 0.8143 (p0) cc_final: 0.7873 (p0) REVERT: E 44 ARG cc_start: 0.8275 (tpt-90) cc_final: 0.8036 (tpt-90) REVERT: E 46 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9068 (tm-30) REVERT: E 92 ASP cc_start: 0.7609 (p0) cc_final: 0.7351 (p0) REVERT: E 131 ASP cc_start: 0.9112 (m-30) cc_final: 0.8583 (m-30) REVERT: F 31 LEU cc_start: 0.9200 (mm) cc_final: 0.8961 (tp) REVERT: F 60 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8531 (mt-10) REVERT: F 86 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8415 (tp40) REVERT: F 110 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8167 (mm-30) REVERT: G 21 ASP cc_start: 0.8323 (p0) cc_final: 0.7850 (p0) REVERT: G 29 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8274 (tm-30) REVERT: G 70 GLU cc_start: 0.8764 (mm-30) cc_final: 0.7740 (tp30) REVERT: G 86 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8687 (mm-40) REVERT: G 92 ASP cc_start: 0.8843 (p0) cc_final: 0.8590 (p0) REVERT: G 132 ASP cc_start: 0.8643 (m-30) cc_final: 0.8115 (t70) REVERT: H 17 ASN cc_start: 0.9112 (m-40) cc_final: 0.8865 (m110) REVERT: H 31 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8986 (tp) REVERT: H 44 ARG cc_start: 0.9062 (ptm-80) cc_final: 0.8619 (ttt180) REVERT: H 105 ASP cc_start: 0.9092 (m-30) cc_final: 0.8856 (m-30) REVERT: H 116 ARG cc_start: 0.8771 (tpp80) cc_final: 0.8525 (tpp80) REVERT: I 13 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8536 (mt-10) REVERT: I 17 ASN cc_start: 0.9558 (m-40) cc_final: 0.9262 (m-40) REVERT: I 35 PHE cc_start: 0.9675 (t80) cc_final: 0.8993 (t80) REVERT: I 38 MET cc_start: 0.8998 (tmm) cc_final: 0.8741 (tmm) REVERT: I 39 CYS cc_start: 0.9097 (p) cc_final: 0.8565 (p) REVERT: I 59 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9374 (tp) REVERT: I 60 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8638 (mt-10) REVERT: I 76 LYS cc_start: 0.9438 (mmmm) cc_final: 0.9230 (mmmm) REVERT: I 89 LYS cc_start: 0.9467 (ttpp) cc_final: 0.8709 (ttpp) REVERT: I 99 TYR cc_start: 0.8547 (t80) cc_final: 0.8220 (t80) REVERT: I 116 ARG cc_start: 0.8480 (mmm160) cc_final: 0.8029 (mmm160) REVERT: J 13 GLU cc_start: 0.8404 (tp30) cc_final: 0.8018 (tp30) REVERT: J 21 ASP cc_start: 0.8511 (p0) cc_final: 0.8071 (p0) REVERT: J 27 GLU cc_start: 0.7058 (mp0) cc_final: 0.6839 (mp0) REVERT: J 34 GLU cc_start: 0.8688 (tt0) cc_final: 0.8298 (tt0) REVERT: J 44 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8252 (mtp180) REVERT: J 69 LYS cc_start: 0.9593 (OUTLIER) cc_final: 0.9391 (ttpp) REVERT: J 70 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8325 (mm-30) REVERT: J 83 GLU cc_start: 0.7842 (pp20) cc_final: 0.7592 (tm-30) REVERT: J 92 ASP cc_start: 0.8962 (p0) cc_final: 0.8618 (p0) REVERT: J 99 TYR cc_start: 0.8948 (t80) cc_final: 0.8554 (t80) REVERT: J 110 GLU cc_start: 0.8945 (tt0) cc_final: 0.8579 (tt0) REVERT: J 112 LYS cc_start: 0.9392 (mtmm) cc_final: 0.8942 (mttp) REVERT: K 69 LYS cc_start: 0.9717 (tttp) cc_final: 0.9425 (ttmm) REVERT: K 79 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8879 (mmtp) REVERT: K 86 GLN cc_start: 0.8853 (tp40) cc_final: 0.8490 (tp-100) REVERT: L 17 ASN cc_start: 0.9545 (m-40) cc_final: 0.9230 (m-40) REVERT: L 21 ASP cc_start: 0.7989 (p0) cc_final: 0.7559 (p0) REVERT: L 38 MET cc_start: 0.9040 (tmm) cc_final: 0.8793 (tmm) REVERT: L 39 CYS cc_start: 0.9226 (p) cc_final: 0.8581 (p) REVERT: L 60 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8606 (mt-10) REVERT: L 83 GLU cc_start: 0.7865 (mp0) cc_final: 0.7627 (mp0) REVERT: L 86 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8878 (tp40) REVERT: M 17 ASN cc_start: 0.9452 (m-40) cc_final: 0.9209 (m110) REVERT: M 70 GLU cc_start: 0.8830 (tp30) cc_final: 0.7784 (tp30) REVERT: M 73 ARG cc_start: 0.9194 (tmm-80) cc_final: 0.8602 (ttp80) REVERT: M 75 ASP cc_start: 0.8963 (p0) cc_final: 0.8727 (p0) REVERT: M 83 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7399 (pp20) REVERT: M 86 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8347 (mm110) REVERT: M 106 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8510 (mp0) REVERT: M 116 ARG cc_start: 0.8806 (tpp80) cc_final: 0.8474 (tpp80) REVERT: M 131 ASP cc_start: 0.8818 (t0) cc_final: 0.8479 (t0) REVERT: M 132 ASP cc_start: 0.8972 (m-30) cc_final: 0.8259 (m-30) REVERT: N 39 CYS cc_start: 0.9703 (m) cc_final: 0.9174 (m) REVERT: N 98 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8851 (p0) REVERT: N 105 ASP cc_start: 0.9294 (m-30) cc_final: 0.8990 (m-30) REVERT: O 13 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8892 (pt0) REVERT: O 21 ASP cc_start: 0.7669 (p0) cc_final: 0.7270 (p0) REVERT: O 60 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8434 (mt-10) REVERT: O 94 THR cc_start: 0.9219 (m) cc_final: 0.8947 (p) REVERT: O 97 MET cc_start: 0.8962 (mmm) cc_final: 0.8675 (mmm) REVERT: O 99 TYR cc_start: 0.8559 (t80) cc_final: 0.8263 (t80) REVERT: O 110 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8498 (mm-30) REVERT: a 1 MET cc_start: 0.9195 (tmm) cc_final: 0.8799 (tmm) REVERT: a 112 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8655 (mm-30) REVERT: b 1 MET cc_start: 0.8051 (tpt) cc_final: 0.7229 (tpt) REVERT: b 55 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8726 (t) REVERT: b 91 VAL cc_start: 0.9489 (t) cc_final: 0.9234 (p) REVERT: c 3 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7444 (ttp80) REVERT: c 58 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7177 (p0) REVERT: c 74 LYS cc_start: 0.7581 (tmtt) cc_final: 0.7377 (tptp) REVERT: c 79 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.8021 (t) REVERT: c 94 GLU cc_start: 0.8622 (tt0) cc_final: 0.8382 (tt0) REVERT: d 29 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8594 (p) REVERT: d 97 ILE cc_start: 0.4867 (OUTLIER) cc_final: 0.4602 (mp) REVERT: e 30 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7025 (p90) REVERT: e 77 SER cc_start: 0.9276 (m) cc_final: 0.8865 (t) REVERT: f 3 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7880 (tmm-80) REVERT: f 27 ASN cc_start: 0.8822 (m-40) cc_final: 0.8425 (m-40) REVERT: f 109 ASN cc_start: 0.8746 (m110) cc_final: 0.8458 (m110) REVERT: g 48 ASN cc_start: 0.9064 (t0) cc_final: 0.8843 (t0) REVERT: g 50 GLU cc_start: 0.7839 (pm20) cc_final: 0.7419 (pm20) REVERT: g 86 ASP cc_start: 0.8499 (m-30) cc_final: 0.8065 (t0) REVERT: h 1 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6264 (tmm) REVERT: h 12 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8027 (p0) REVERT: i 1 MET cc_start: 0.7144 (ttm) cc_final: 0.6836 (ttm) REVERT: j 1 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6122 (ttm) REVERT: j 12 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8076 (p0) REVERT: j 48 ASN cc_start: 0.9094 (t0) cc_final: 0.8721 (t0) REVERT: j 50 GLU cc_start: 0.8420 (pm20) cc_final: 0.7452 (pm20) REVERT: j 75 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8831 (mmmm) REVERT: j 101 ASP cc_start: 0.8227 (p0) cc_final: 0.7898 (p0) REVERT: k 5 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8209 (mtmm) REVERT: m 13 ASP cc_start: 0.7978 (m-30) cc_final: 0.7765 (m-30) REVERT: m 29 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7849 (p) REVERT: m 48 ASN cc_start: 0.9140 (t0) cc_final: 0.8686 (t0) REVERT: m 50 GLU cc_start: 0.8439 (mp0) cc_final: 0.7403 (pm20) REVERT: m 54 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.6799 (p0) REVERT: m 74 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8117 (tptp) REVERT: n 100 THR cc_start: 0.6706 (OUTLIER) cc_final: 0.6459 (p) REVERT: n 111 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9124 (pp) REVERT: o 1 MET cc_start: 0.7915 (ttp) cc_final: 0.7667 (tmm) REVERT: o 54 ASN cc_start: 0.8293 (p0) cc_final: 0.7846 (p0) REVERT: o 65 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.6022 (t80) REVERT: o 77 SER cc_start: 0.9391 (p) cc_final: 0.8834 (p) REVERT: o 103 GLU cc_start: 0.7632 (tp30) cc_final: 0.7337 (tp30) outliers start: 258 outliers final: 183 residues processed: 1305 average time/residue: 0.4364 time to fit residues: 881.3069 Evaluate side-chains 1262 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1052 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 112 LYS Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain a residue 10 HIS Chi-restraints excluded: chain a residue 13 ASP Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 48 ASN Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 106 ASN Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 86 ASP Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 42 HIS Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 106 ASN Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 48 ASN Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 108 LEU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 17 ILE Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 100 THR Chi-restraints excluded: chain n residue 104 TYR Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 215 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 284 optimal weight: 30.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 47 GLN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 73 ASN ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31470 Z= 0.276 Angle : 0.820 13.331 42780 Z= 0.425 Chirality : 0.047 0.286 4995 Planarity : 0.005 0.064 5565 Dihedral : 7.334 57.399 4248 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.96 % Favored : 90.91 % Rotamer: Outliers : 7.49 % Allowed : 29.28 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 3795 helix: 0.24 (0.12), residues: 1612 sheet: -0.39 (0.21), residues: 616 loop : -2.21 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 16 HIS 0.008 0.001 HIS e 76 PHE 0.033 0.002 PHE c 89 TYR 0.035 0.002 TYR m 110 ARG 0.011 0.001 ARG a 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1379 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1115 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8362 (tp30) cc_final: 0.7789 (tp30) REVERT: A 17 ASN cc_start: 0.8761 (m110) cc_final: 0.8024 (m110) REVERT: A 38 MET cc_start: 0.9131 (tmm) cc_final: 0.8608 (tmm) REVERT: A 106 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 122 VAL cc_start: 0.9494 (OUTLIER) cc_final: 0.8900 (p) REVERT: A 124 ASP cc_start: 0.9156 (t0) cc_final: 0.8879 (t0) REVERT: A 132 ASP cc_start: 0.8965 (m-30) cc_final: 0.8096 (t70) REVERT: B 77 LEU cc_start: 0.9748 (OUTLIER) cc_final: 0.9485 (tt) REVERT: B 105 ASP cc_start: 0.9059 (m-30) cc_final: 0.8557 (p0) REVERT: B 116 ARG cc_start: 0.9059 (tpp80) cc_final: 0.8737 (tpp80) REVERT: B 124 ASP cc_start: 0.8660 (t0) cc_final: 0.8276 (t0) REVERT: C 13 GLU cc_start: 0.8648 (tp30) cc_final: 0.7686 (tp30) REVERT: C 17 ASN cc_start: 0.9332 (m-40) cc_final: 0.8323 (m-40) REVERT: C 38 MET cc_start: 0.9008 (tmm) cc_final: 0.8607 (tmm) REVERT: C 39 CYS cc_start: 0.9112 (p) cc_final: 0.8782 (p) REVERT: C 60 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8440 (mt-10) REVERT: C 86 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8239 (tp40) REVERT: D 21 ASP cc_start: 0.7533 (p0) cc_final: 0.7212 (p0) REVERT: D 44 ARG cc_start: 0.8736 (ptm160) cc_final: 0.8311 (ptm160) REVERT: D 60 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8859 (mm-30) REVERT: D 69 LYS cc_start: 0.9625 (OUTLIER) cc_final: 0.9350 (ttpp) REVERT: D 70 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8324 (tp30) REVERT: D 74 LEU cc_start: 0.9759 (mm) cc_final: 0.9493 (mm) REVERT: D 112 LYS cc_start: 0.9409 (mtmm) cc_final: 0.9009 (mtmm) REVERT: D 132 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7509 (t0) REVERT: E 17 ASN cc_start: 0.9354 (m-40) cc_final: 0.9108 (m-40) REVERT: E 21 ASP cc_start: 0.8215 (p0) cc_final: 0.7954 (p0) REVERT: E 44 ARG cc_start: 0.8240 (tpt-90) cc_final: 0.7999 (tpt-90) REVERT: E 92 ASP cc_start: 0.7668 (p0) cc_final: 0.7117 (p0) REVERT: E 105 ASP cc_start: 0.9082 (m-30) cc_final: 0.8653 (p0) REVERT: E 136 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7592 (tmm-80) REVERT: F 60 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8396 (mt-10) REVERT: F 86 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8433 (tp40) REVERT: F 110 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8226 (mm-30) REVERT: G 21 ASP cc_start: 0.8343 (p0) cc_final: 0.7991 (p0) REVERT: G 29 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8401 (tm-30) REVERT: G 44 ARG cc_start: 0.8440 (ptm160) cc_final: 0.7356 (ttm-80) REVERT: G 70 GLU cc_start: 0.8788 (mm-30) cc_final: 0.7899 (tp30) REVERT: G 74 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9321 (mm) REVERT: G 92 ASP cc_start: 0.8879 (p0) cc_final: 0.8579 (p0) REVERT: G 132 ASP cc_start: 0.8580 (m-30) cc_final: 0.8012 (t70) REVERT: H 31 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9022 (tp) REVERT: H 44 ARG cc_start: 0.9057 (ptm-80) cc_final: 0.8612 (ttt180) REVERT: H 105 ASP cc_start: 0.9118 (m-30) cc_final: 0.8861 (m-30) REVERT: H 131 ASP cc_start: 0.9153 (p0) cc_final: 0.8944 (p0) REVERT: I 13 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8534 (mt-10) REVERT: I 17 ASN cc_start: 0.9557 (m-40) cc_final: 0.9254 (m-40) REVERT: I 21 ASP cc_start: 0.8166 (p0) cc_final: 0.7849 (p0) REVERT: I 38 MET cc_start: 0.9018 (tmm) cc_final: 0.8756 (tmm) REVERT: I 39 CYS cc_start: 0.9101 (p) cc_final: 0.8611 (p) REVERT: I 53 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9146 (tt) REVERT: I 56 LEU cc_start: 0.9184 (tt) cc_final: 0.8861 (mt) REVERT: I 60 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8690 (mt-10) REVERT: I 95 MET cc_start: 0.8543 (mmm) cc_final: 0.8021 (mmm) REVERT: I 99 TYR cc_start: 0.8624 (t80) cc_final: 0.8241 (t80) REVERT: I 116 ARG cc_start: 0.8502 (mmm160) cc_final: 0.8150 (mmm160) REVERT: J 13 GLU cc_start: 0.8439 (tp30) cc_final: 0.8132 (tp30) REVERT: J 21 ASP cc_start: 0.8493 (p0) cc_final: 0.8110 (p0) REVERT: J 27 GLU cc_start: 0.7223 (mp0) cc_final: 0.6994 (mp0) REVERT: J 34 GLU cc_start: 0.8675 (tt0) cc_final: 0.8297 (tt0) REVERT: J 44 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8243 (mtp180) REVERT: J 69 LYS cc_start: 0.9599 (OUTLIER) cc_final: 0.9392 (ttpp) REVERT: J 70 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8283 (mm-30) REVERT: J 74 LEU cc_start: 0.9737 (mp) cc_final: 0.9512 (mp) REVERT: J 83 GLU cc_start: 0.7855 (pp20) cc_final: 0.7621 (tm-30) REVERT: J 86 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8825 (mm-40) REVERT: K 69 LYS cc_start: 0.9723 (tttp) cc_final: 0.9427 (ttmm) REVERT: K 86 GLN cc_start: 0.8882 (tp40) cc_final: 0.8534 (tp-100) REVERT: K 92 ASP cc_start: 0.8191 (p0) cc_final: 0.7821 (p0) REVERT: K 105 ASP cc_start: 0.9302 (m-30) cc_final: 0.8857 (p0) REVERT: K 112 LYS cc_start: 0.9472 (mtmm) cc_final: 0.8935 (mtmm) REVERT: L 17 ASN cc_start: 0.9559 (m-40) cc_final: 0.9239 (m-40) REVERT: L 21 ASP cc_start: 0.8004 (p0) cc_final: 0.7531 (p0) REVERT: L 35 PHE cc_start: 0.9696 (t80) cc_final: 0.8942 (t80) REVERT: L 38 MET cc_start: 0.8978 (tmm) cc_final: 0.8753 (tmm) REVERT: L 39 CYS cc_start: 0.9226 (p) cc_final: 0.8463 (p) REVERT: L 42 PHE cc_start: 0.9271 (m-80) cc_final: 0.9042 (m-80) REVERT: L 83 GLU cc_start: 0.7992 (mp0) cc_final: 0.7690 (mp0) REVERT: L 86 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8905 (tp40) REVERT: L 110 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8670 (tp30) REVERT: L 116 ARG cc_start: 0.8470 (mmm160) cc_final: 0.8079 (mmp80) REVERT: M 17 ASN cc_start: 0.9459 (m-40) cc_final: 0.9217 (m110) REVERT: M 69 LYS cc_start: 0.9604 (ttpp) cc_final: 0.9370 (ttpp) REVERT: M 73 ARG cc_start: 0.9211 (tmm-80) cc_final: 0.8679 (ttp80) REVERT: M 75 ASP cc_start: 0.9015 (p0) cc_final: 0.8770 (p0) REVERT: M 83 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7519 (pp20) REVERT: M 106 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8495 (mp0) REVERT: M 116 ARG cc_start: 0.8781 (tpp80) cc_final: 0.8451 (tpp80) REVERT: M 131 ASP cc_start: 0.8830 (t0) cc_final: 0.8507 (t0) REVERT: M 132 ASP cc_start: 0.8920 (m-30) cc_final: 0.8268 (m-30) REVERT: N 39 CYS cc_start: 0.9676 (m) cc_final: 0.9170 (m) REVERT: N 92 ASP cc_start: 0.8056 (p0) cc_final: 0.7492 (p0) REVERT: N 98 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8853 (p0) REVERT: N 105 ASP cc_start: 0.9298 (m-30) cc_final: 0.8998 (m-30) REVERT: O 21 ASP cc_start: 0.7676 (p0) cc_final: 0.7269 (p0) REVERT: O 60 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8386 (mt-10) REVERT: O 69 LYS cc_start: 0.9466 (ttmt) cc_final: 0.9238 (ttpp) REVERT: O 94 THR cc_start: 0.9181 (m) cc_final: 0.8913 (p) REVERT: O 97 MET cc_start: 0.8981 (mmm) cc_final: 0.8657 (mmm) REVERT: O 99 TYR cc_start: 0.8586 (t80) cc_final: 0.8314 (t80) REVERT: O 110 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8641 (mm-30) REVERT: a 1 MET cc_start: 0.9181 (tmm) cc_final: 0.8770 (tmm) REVERT: a 103 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6372 (pm20) REVERT: a 112 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8737 (mm-30) REVERT: b 1 MET cc_start: 0.8211 (tpt) cc_final: 0.7361 (tpt) REVERT: b 55 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8802 (t) REVERT: b 91 VAL cc_start: 0.9514 (t) cc_final: 0.9250 (p) REVERT: b 121 ASN cc_start: 0.9018 (m110) cc_final: 0.8753 (m110) REVERT: c 3 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7328 (ttp80) REVERT: c 58 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7203 (p0) REVERT: c 94 GLU cc_start: 0.8616 (tt0) cc_final: 0.8359 (tt0) REVERT: c 114 TYR cc_start: 0.8946 (t80) cc_final: 0.8584 (t80) REVERT: c 117 ASP cc_start: 0.8953 (m-30) cc_final: 0.8583 (p0) REVERT: d 29 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8694 (p) REVERT: d 50 GLU cc_start: 0.7814 (tp30) cc_final: 0.7567 (tp30) REVERT: d 54 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8706 (m-40) REVERT: d 97 ILE cc_start: 0.5107 (OUTLIER) cc_final: 0.4841 (mp) REVERT: e 30 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7134 (p90) REVERT: e 77 SER cc_start: 0.9271 (m) cc_final: 0.8870 (t) REVERT: f 3 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7932 (ttp-110) REVERT: f 27 ASN cc_start: 0.8864 (m-40) cc_final: 0.8645 (m-40) REVERT: f 105 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9033 (m) REVERT: f 109 ASN cc_start: 0.8881 (m110) cc_final: 0.8499 (m110) REVERT: g 48 ASN cc_start: 0.9091 (t0) cc_final: 0.8866 (t0) REVERT: g 86 ASP cc_start: 0.8809 (m-30) cc_final: 0.8556 (t70) REVERT: h 12 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8027 (p0) REVERT: h 74 LYS cc_start: 0.9437 (mmtp) cc_final: 0.9197 (mmmm) REVERT: i 1 MET cc_start: 0.6892 (ttm) cc_final: 0.6603 (ttm) REVERT: j 12 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8128 (p0) REVERT: j 48 ASN cc_start: 0.9146 (t0) cc_final: 0.8773 (t0) REVERT: j 50 GLU cc_start: 0.8402 (pm20) cc_final: 0.7422 (pm20) REVERT: j 75 LYS cc_start: 0.9297 (mmmm) cc_final: 0.8983 (mmmm) REVERT: j 101 ASP cc_start: 0.8322 (p0) cc_final: 0.7947 (p0) REVERT: j 112 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8735 (tm-30) REVERT: k 5 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8233 (mtmm) REVERT: l 50 GLU cc_start: 0.8443 (tp30) cc_final: 0.8162 (tp30) REVERT: m 2 ARG cc_start: 0.5662 (OUTLIER) cc_final: 0.5225 (mtp180) REVERT: m 13 ASP cc_start: 0.7925 (m-30) cc_final: 0.7677 (m-30) REVERT: m 29 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8024 (p) REVERT: m 48 ASN cc_start: 0.9159 (t0) cc_final: 0.8681 (t0) REVERT: m 74 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8208 (tptp) REVERT: n 111 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9138 (pp) REVERT: o 14 GLN cc_start: 0.9424 (mp10) cc_final: 0.9186 (mm-40) REVERT: o 50 GLU cc_start: 0.7569 (tp30) cc_final: 0.7072 (tp30) REVERT: o 54 ASN cc_start: 0.8330 (p0) cc_final: 0.7875 (p0) REVERT: o 65 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.6049 (t80) REVERT: o 77 SER cc_start: 0.9404 (p) cc_final: 0.8897 (p) REVERT: o 103 GLU cc_start: 0.7914 (tp30) cc_final: 0.7376 (tm-30) outliers start: 264 outliers final: 205 residues processed: 1275 average time/residue: 0.4360 time to fit residues: 858.7280 Evaluate side-chains 1281 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1049 time to evaluate : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 112 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain a residue 10 HIS Chi-restraints excluded: chain a residue 13 ASP Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 48 ASN Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 103 GLU Chi-restraints excluded: chain c residue 106 ASN Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 54 ASN Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 86 ASP Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 42 HIS Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 42 HIS Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 106 ASN Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 47 GLN Chi-restraints excluded: chain i residue 48 ASN Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 108 LEU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 70 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 2 ARG Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 HIS Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 75 LYS Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 17 ILE Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 104 TYR Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 8.9990 chunk 346 optimal weight: 7.9990 chunk 315 optimal weight: 0.2980 chunk 336 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 103 optimal weight: 0.0170 chunk 304 optimal weight: 6.9990 chunk 318 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 overall best weight: 3.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 ASN ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 18 ASN ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 123 GLN ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 31470 Z= 0.272 Angle : 0.841 12.471 42780 Z= 0.436 Chirality : 0.048 0.286 4995 Planarity : 0.005 0.068 5565 Dihedral : 7.359 57.611 4246 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.88 % Favored : 90.99 % Rotamer: Outliers : 7.18 % Allowed : 30.01 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3795 helix: 0.21 (0.12), residues: 1612 sheet: -0.32 (0.21), residues: 618 loop : -2.16 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 16 HIS 0.007 0.001 HIS e 76 PHE 0.037 0.002 PHE A 49 TYR 0.032 0.002 TYR m 110 ARG 0.015 0.001 ARG N 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1103 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8363 (tp30) cc_final: 0.7777 (tp30) REVERT: A 17 ASN cc_start: 0.8770 (m110) cc_final: 0.8032 (m110) REVERT: A 38 MET cc_start: 0.9157 (tmm) cc_final: 0.8639 (tmm) REVERT: A 53 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9133 (mm) REVERT: A 92 ASP cc_start: 0.8879 (p0) cc_final: 0.8575 (p0) REVERT: A 106 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8324 (mt-10) REVERT: A 112 LYS cc_start: 0.9323 (mtmm) cc_final: 0.9112 (mtmm) REVERT: A 122 VAL cc_start: 0.9498 (OUTLIER) cc_final: 0.8899 (p) REVERT: A 124 ASP cc_start: 0.9160 (t0) cc_final: 0.8868 (t0) REVERT: A 132 ASP cc_start: 0.8925 (m-30) cc_final: 0.8031 (t70) REVERT: B 77 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9518 (tt) REVERT: B 116 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8704 (tpp80) REVERT: C 13 GLU cc_start: 0.8647 (tp30) cc_final: 0.7604 (tp30) REVERT: C 17 ASN cc_start: 0.9332 (m-40) cc_final: 0.8204 (m-40) REVERT: C 35 PHE cc_start: 0.9653 (t80) cc_final: 0.8978 (t80) REVERT: C 38 MET cc_start: 0.9012 (tmm) cc_final: 0.8626 (tmm) REVERT: C 39 CYS cc_start: 0.9189 (p) cc_final: 0.8782 (p) REVERT: C 86 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8204 (tp40) REVERT: C 92 ASP cc_start: 0.8421 (p0) cc_final: 0.8213 (p0) REVERT: D 21 ASP cc_start: 0.7506 (p0) cc_final: 0.7169 (p0) REVERT: D 60 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8836 (mm-30) REVERT: D 69 LYS cc_start: 0.9638 (OUTLIER) cc_final: 0.9374 (ttpp) REVERT: D 132 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7523 (t0) REVERT: E 17 ASN cc_start: 0.9357 (m-40) cc_final: 0.9119 (m-40) REVERT: E 21 ASP cc_start: 0.8177 (p0) cc_final: 0.7925 (p0) REVERT: E 92 ASP cc_start: 0.7595 (p0) cc_final: 0.7137 (t70) REVERT: E 124 ASP cc_start: 0.8603 (t70) cc_final: 0.8378 (t70) REVERT: E 136 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7509 (tmm-80) REVERT: F 60 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8421 (mt-10) REVERT: F 86 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8408 (tp40) REVERT: F 90 VAL cc_start: 0.9153 (t) cc_final: 0.8829 (m) REVERT: F 110 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8227 (mm-30) REVERT: F 116 ARG cc_start: 0.8547 (mmm160) cc_final: 0.8329 (mmp80) REVERT: G 21 ASP cc_start: 0.8370 (p0) cc_final: 0.8005 (p0) REVERT: G 29 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8397 (tm-30) REVERT: G 44 ARG cc_start: 0.8430 (ptm160) cc_final: 0.7429 (ttm-80) REVERT: G 70 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8024 (tp30) REVERT: G 74 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9431 (mm) REVERT: G 92 ASP cc_start: 0.8875 (p0) cc_final: 0.8572 (p0) REVERT: G 124 ASP cc_start: 0.8958 (p0) cc_final: 0.8674 (t0) REVERT: G 132 ASP cc_start: 0.8590 (m-30) cc_final: 0.8012 (t70) REVERT: H 17 ASN cc_start: 0.8978 (m-40) cc_final: 0.8759 (m110) REVERT: H 31 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9035 (tp) REVERT: H 44 ARG cc_start: 0.9042 (ptm-80) cc_final: 0.8597 (ttt180) REVERT: H 105 ASP cc_start: 0.9071 (m-30) cc_final: 0.8814 (m-30) REVERT: I 17 ASN cc_start: 0.9557 (m-40) cc_final: 0.9245 (m-40) REVERT: I 35 PHE cc_start: 0.9675 (t80) cc_final: 0.9033 (t80) REVERT: I 38 MET cc_start: 0.9009 (tmm) cc_final: 0.8747 (tmm) REVERT: I 39 CYS cc_start: 0.9104 (p) cc_final: 0.8620 (p) REVERT: I 60 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8670 (mt-10) REVERT: I 89 LYS cc_start: 0.9501 (ttpp) cc_final: 0.8753 (ttpp) REVERT: I 99 TYR cc_start: 0.8637 (t80) cc_final: 0.8320 (t80) REVERT: I 116 ARG cc_start: 0.8375 (mmm160) cc_final: 0.7961 (mmm160) REVERT: J 13 GLU cc_start: 0.8424 (tp30) cc_final: 0.8105 (tp30) REVERT: J 21 ASP cc_start: 0.8477 (p0) cc_final: 0.8082 (p0) REVERT: J 34 GLU cc_start: 0.8667 (tt0) cc_final: 0.8291 (tt0) REVERT: J 69 LYS cc_start: 0.9594 (OUTLIER) cc_final: 0.9386 (ttpp) REVERT: J 70 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8240 (mm-30) REVERT: J 74 LEU cc_start: 0.9732 (mp) cc_final: 0.9530 (mp) REVERT: J 83 GLU cc_start: 0.7863 (pp20) cc_final: 0.7596 (tm-30) REVERT: J 112 LYS cc_start: 0.9379 (mtmm) cc_final: 0.8897 (mttp) REVERT: K 69 LYS cc_start: 0.9705 (tttp) cc_final: 0.9402 (ttmm) REVERT: K 75 ASP cc_start: 0.8929 (t0) cc_final: 0.8473 (t0) REVERT: K 79 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8153 (mttp) REVERT: K 86 GLN cc_start: 0.8864 (tp40) cc_final: 0.8520 (tp-100) REVERT: L 17 ASN cc_start: 0.9573 (m-40) cc_final: 0.9264 (m-40) REVERT: L 21 ASP cc_start: 0.7952 (p0) cc_final: 0.7451 (p0) REVERT: L 38 MET cc_start: 0.8970 (tmm) cc_final: 0.8747 (tmm) REVERT: L 39 CYS cc_start: 0.9250 (p) cc_final: 0.8489 (p) REVERT: L 83 GLU cc_start: 0.7875 (mp0) cc_final: 0.7618 (mp0) REVERT: L 86 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8880 (tp40) REVERT: L 110 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8684 (tp30) REVERT: L 116 ARG cc_start: 0.8393 (mmm160) cc_final: 0.7905 (mmp80) REVERT: M 17 ASN cc_start: 0.9466 (m-40) cc_final: 0.9230 (m110) REVERT: M 69 LYS cc_start: 0.9616 (ttpp) cc_final: 0.9390 (ttpp) REVERT: M 73 ARG cc_start: 0.9190 (tmm-80) cc_final: 0.8631 (ttp80) REVERT: M 75 ASP cc_start: 0.8993 (p0) cc_final: 0.8743 (p0) REVERT: M 83 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7513 (pp20) REVERT: M 106 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8561 (mt-10) REVERT: M 116 ARG cc_start: 0.8820 (tpp80) cc_final: 0.8601 (tpp80) REVERT: M 131 ASP cc_start: 0.8833 (t0) cc_final: 0.8540 (t0) REVERT: M 132 ASP cc_start: 0.8901 (m-30) cc_final: 0.8217 (m-30) REVERT: N 39 CYS cc_start: 0.9617 (m) cc_final: 0.9147 (m) REVERT: N 92 ASP cc_start: 0.7912 (p0) cc_final: 0.7606 (p0) REVERT: N 98 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8835 (p0) REVERT: N 105 ASP cc_start: 0.9285 (m-30) cc_final: 0.8975 (m-30) REVERT: O 21 ASP cc_start: 0.7666 (p0) cc_final: 0.7261 (p0) REVERT: O 60 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8434 (mt-10) REVERT: O 69 LYS cc_start: 0.9458 (ttmt) cc_final: 0.9239 (ttpp) REVERT: O 94 THR cc_start: 0.9247 (m) cc_final: 0.8962 (p) REVERT: O 97 MET cc_start: 0.8998 (mmm) cc_final: 0.8679 (mmm) REVERT: O 99 TYR cc_start: 0.8592 (t80) cc_final: 0.8325 (t80) REVERT: O 116 ARG cc_start: 0.8275 (mmp80) cc_final: 0.8020 (mmp80) REVERT: a 1 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8745 (tmm) REVERT: a 103 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6418 (pm20) REVERT: a 112 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8790 (mm-30) REVERT: b 91 VAL cc_start: 0.9525 (t) cc_final: 0.9263 (p) REVERT: c 3 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7305 (ttp80) REVERT: c 58 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7469 (p0) REVERT: c 69 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8708 (p) REVERT: c 94 GLU cc_start: 0.8710 (tt0) cc_final: 0.8489 (tt0) REVERT: c 114 TYR cc_start: 0.8934 (t80) cc_final: 0.8694 (t80) REVERT: d 18 ASN cc_start: 0.8964 (p0) cc_final: 0.8689 (p0) REVERT: d 29 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8710 (p) REVERT: d 50 GLU cc_start: 0.7807 (tp30) cc_final: 0.7540 (tp30) REVERT: d 54 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8711 (m-40) REVERT: d 97 ILE cc_start: 0.5619 (OUTLIER) cc_final: 0.5385 (mp) REVERT: e 30 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7163 (p90) REVERT: f 3 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7959 (ttp-110) REVERT: f 109 ASN cc_start: 0.8880 (m110) cc_final: 0.8522 (m110) REVERT: g 48 ASN cc_start: 0.9139 (t0) cc_final: 0.8905 (t0) REVERT: g 74 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7809 (tptp) REVERT: g 86 ASP cc_start: 0.8851 (m-30) cc_final: 0.8559 (t70) REVERT: h 12 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8006 (p0) REVERT: h 36 TYR cc_start: 0.9224 (m-10) cc_final: 0.9022 (m-10) REVERT: i 1 MET cc_start: 0.6787 (ttm) cc_final: 0.6512 (ttm) REVERT: j 1 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.5484 (ttt) REVERT: j 12 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8172 (p0) REVERT: j 48 ASN cc_start: 0.9098 (t0) cc_final: 0.8709 (t0) REVERT: j 50 GLU cc_start: 0.8401 (pm20) cc_final: 0.7410 (pm20) REVERT: j 75 LYS cc_start: 0.9270 (mmmm) cc_final: 0.9014 (mmmm) REVERT: j 101 ASP cc_start: 0.8289 (p0) cc_final: 0.7873 (p0) REVERT: j 112 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8776 (tm-30) REVERT: k 5 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8200 (mtmm) REVERT: l 12 ASP cc_start: 0.8374 (p0) cc_final: 0.8162 (p0) REVERT: l 46 ASP cc_start: 0.8697 (p0) cc_final: 0.8206 (p0) REVERT: l 48 ASN cc_start: 0.9386 (m-40) cc_final: 0.8763 (p0) REVERT: l 50 GLU cc_start: 0.8475 (tp30) cc_final: 0.8041 (tp30) REVERT: l 93 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8362 (tpt170) REVERT: m 13 ASP cc_start: 0.7921 (m-30) cc_final: 0.7545 (m-30) REVERT: m 29 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8075 (p) REVERT: m 48 ASN cc_start: 0.9176 (t0) cc_final: 0.8694 (t0) REVERT: m 74 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8247 (tptp) REVERT: n 104 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: n 111 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9151 (pp) REVERT: o 14 GLN cc_start: 0.9414 (mp10) cc_final: 0.9159 (mm-40) REVERT: o 50 GLU cc_start: 0.7616 (tp30) cc_final: 0.7088 (tp30) REVERT: o 54 ASN cc_start: 0.8426 (p0) cc_final: 0.7838 (p0) REVERT: o 65 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.6114 (t80) REVERT: o 77 SER cc_start: 0.9407 (p) cc_final: 0.8878 (p) REVERT: o 103 GLU cc_start: 0.7882 (tp30) cc_final: 0.7429 (tp30) outliers start: 253 outliers final: 201 residues processed: 1252 average time/residue: 0.4340 time to fit residues: 842.5472 Evaluate side-chains 1295 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1064 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 130 TYR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 112 LYS Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 10 HIS Chi-restraints excluded: chain a residue 13 ASP Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 48 ASN Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 103 GLU Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 54 ASN Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 86 ASP Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 42 HIS Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 42 HIS Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 65 TYR Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 106 ASN Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 48 ASN Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 108 LEU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 70 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 47 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 HIS Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 75 LYS Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 17 ILE Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 104 TYR Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 42 HIS Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 4.9990 chunk 356 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 168 optimal weight: 0.4980 chunk 247 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 chunk 297 optimal weight: 0.0170 chunk 30 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 overall best weight: 2.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 ASN f 58 ASN i 47 GLN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 GLN j 73 ASN l 73 ASN ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31470 Z= 0.250 Angle : 0.869 13.709 42780 Z= 0.447 Chirality : 0.049 0.298 4995 Planarity : 0.005 0.072 5565 Dihedral : 7.273 57.912 4240 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.62 % Favored : 91.23 % Rotamer: Outliers : 6.50 % Allowed : 31.06 % Favored : 62.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3795 helix: 0.16 (0.12), residues: 1612 sheet: -0.15 (0.21), residues: 619 loop : -2.16 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 16 HIS 0.006 0.001 HIS a 76 PHE 0.035 0.002 PHE A 49 TYR 0.037 0.002 TYR m 110 ARG 0.014 0.001 ARG N 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1370 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1141 time to evaluate : 4.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8315 (tp30) cc_final: 0.7744 (tp30) REVERT: A 17 ASN cc_start: 0.8654 (m110) cc_final: 0.7910 (m110) REVERT: A 38 MET cc_start: 0.9155 (tmm) cc_final: 0.8625 (tmm) REVERT: A 92 ASP cc_start: 0.8855 (p0) cc_final: 0.8517 (p0) REVERT: A 106 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 112 LYS cc_start: 0.9345 (mtmm) cc_final: 0.9117 (mtmm) REVERT: A 122 VAL cc_start: 0.9469 (OUTLIER) cc_final: 0.8861 (p) REVERT: A 132 ASP cc_start: 0.8976 (m-30) cc_final: 0.8087 (t70) REVERT: B 75 ASP cc_start: 0.8863 (t0) cc_final: 0.8490 (t0) REVERT: B 77 LEU cc_start: 0.9758 (OUTLIER) cc_final: 0.9517 (tt) REVERT: B 79 LYS cc_start: 0.9198 (mttp) cc_final: 0.8542 (mttm) REVERT: B 105 ASP cc_start: 0.9053 (m-30) cc_final: 0.8514 (p0) REVERT: B 124 ASP cc_start: 0.8537 (t0) cc_final: 0.8121 (t0) REVERT: C 13 GLU cc_start: 0.8608 (tp30) cc_final: 0.7524 (tp30) REVERT: C 17 ASN cc_start: 0.9333 (m-40) cc_final: 0.8052 (m-40) REVERT: C 38 MET cc_start: 0.9007 (tmm) cc_final: 0.8588 (tmm) REVERT: C 39 CYS cc_start: 0.9106 (p) cc_final: 0.8701 (p) REVERT: C 60 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8506 (mt-10) REVERT: C 86 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8365 (tp40) REVERT: C 92 ASP cc_start: 0.8360 (p0) cc_final: 0.7649 (p0) REVERT: D 21 ASP cc_start: 0.7482 (p0) cc_final: 0.7125 (p0) REVERT: D 44 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8360 (ptm160) REVERT: D 60 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8813 (mm-30) REVERT: D 69 LYS cc_start: 0.9620 (OUTLIER) cc_final: 0.9365 (ttpp) REVERT: D 90 VAL cc_start: 0.8726 (m) cc_final: 0.8122 (p) REVERT: D 132 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7377 (t0) REVERT: E 17 ASN cc_start: 0.9345 (m-40) cc_final: 0.9099 (m-40) REVERT: E 21 ASP cc_start: 0.8158 (p0) cc_final: 0.7903 (p0) REVERT: E 44 ARG cc_start: 0.8128 (tpt-90) cc_final: 0.7883 (tpt-90) REVERT: E 92 ASP cc_start: 0.7614 (p0) cc_final: 0.7139 (t0) REVERT: E 104 LYS cc_start: 0.9376 (mmtm) cc_final: 0.9162 (mmtt) REVERT: E 105 ASP cc_start: 0.9088 (m-30) cc_final: 0.8619 (p0) REVERT: E 136 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7481 (tmm-80) REVERT: F 60 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8563 (mt-10) REVERT: F 86 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8385 (tp40) REVERT: F 110 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8235 (mm-30) REVERT: G 21 ASP cc_start: 0.8407 (p0) cc_final: 0.8069 (p0) REVERT: G 29 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8485 (tm-30) REVERT: G 44 ARG cc_start: 0.8405 (ptm160) cc_final: 0.7394 (ttm-80) REVERT: G 70 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8008 (tp30) REVERT: G 74 LEU cc_start: 0.9741 (OUTLIER) cc_final: 0.9341 (mm) REVERT: G 92 ASP cc_start: 0.8900 (p0) cc_final: 0.8527 (p0) REVERT: G 124 ASP cc_start: 0.8959 (p0) cc_final: 0.8659 (t0) REVERT: G 132 ASP cc_start: 0.8466 (m-30) cc_final: 0.7930 (t70) REVERT: H 31 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9021 (tp) REVERT: H 44 ARG cc_start: 0.8997 (ptm-80) cc_final: 0.8411 (ttt180) REVERT: H 89 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8682 (mmmm) REVERT: H 105 ASP cc_start: 0.9053 (m-30) cc_final: 0.8771 (m-30) REVERT: H 124 ASP cc_start: 0.8363 (t70) cc_final: 0.7871 (t70) REVERT: I 13 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8616 (mt-10) REVERT: I 35 PHE cc_start: 0.9649 (t80) cc_final: 0.8984 (t80) REVERT: I 38 MET cc_start: 0.8993 (tmm) cc_final: 0.8723 (tmm) REVERT: I 39 CYS cc_start: 0.9118 (p) cc_final: 0.8630 (p) REVERT: I 60 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8583 (mt-10) REVERT: I 76 LYS cc_start: 0.9363 (mmmm) cc_final: 0.9139 (mmmm) REVERT: I 99 TYR cc_start: 0.8437 (t80) cc_final: 0.8169 (t80) REVERT: I 116 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7626 (mmm160) REVERT: J 21 ASP cc_start: 0.8454 (p0) cc_final: 0.8121 (p0) REVERT: J 34 GLU cc_start: 0.8675 (tt0) cc_final: 0.8218 (tt0) REVERT: J 69 LYS cc_start: 0.9590 (OUTLIER) cc_final: 0.9383 (ttpp) REVERT: J 70 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8190 (mm-30) REVERT: J 74 LEU cc_start: 0.9721 (mp) cc_final: 0.9118 (mt) REVERT: J 83 GLU cc_start: 0.7803 (pp20) cc_final: 0.7507 (tm-30) REVERT: J 99 TYR cc_start: 0.8925 (t80) cc_final: 0.8572 (t80) REVERT: J 110 GLU cc_start: 0.8988 (tt0) cc_final: 0.8509 (tt0) REVERT: J 112 LYS cc_start: 0.9381 (mtmm) cc_final: 0.8947 (mttp) REVERT: K 69 LYS cc_start: 0.9718 (tttp) cc_final: 0.9327 (ttmm) REVERT: K 86 GLN cc_start: 0.8835 (tp40) cc_final: 0.8524 (tp-100) REVERT: K 105 ASP cc_start: 0.9298 (m-30) cc_final: 0.8811 (p0) REVERT: K 112 LYS cc_start: 0.9497 (mttp) cc_final: 0.9157 (mttp) REVERT: L 21 ASP cc_start: 0.7955 (p0) cc_final: 0.7485 (p0) REVERT: L 38 MET cc_start: 0.8933 (tmm) cc_final: 0.8649 (tmm) REVERT: L 39 CYS cc_start: 0.9195 (p) cc_final: 0.8448 (p) REVERT: L 83 GLU cc_start: 0.7887 (mp0) cc_final: 0.7656 (mp0) REVERT: L 86 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8848 (tp40) REVERT: M 17 ASN cc_start: 0.9461 (m-40) cc_final: 0.9196 (m-40) REVERT: M 73 ARG cc_start: 0.9161 (tmm-80) cc_final: 0.8595 (ttp80) REVERT: M 75 ASP cc_start: 0.8964 (p0) cc_final: 0.8703 (p0) REVERT: M 83 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7460 (pp20) REVERT: M 106 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8540 (mt-10) REVERT: M 116 ARG cc_start: 0.8805 (tpp80) cc_final: 0.8598 (tpp80) REVERT: M 131 ASP cc_start: 0.8848 (t0) cc_final: 0.8595 (t0) REVERT: M 132 ASP cc_start: 0.8891 (m-30) cc_final: 0.8374 (m-30) REVERT: N 39 CYS cc_start: 0.9527 (m) cc_final: 0.9112 (m) REVERT: N 92 ASP cc_start: 0.7995 (p0) cc_final: 0.7693 (p0) REVERT: N 98 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8872 (p0) REVERT: N 105 ASP cc_start: 0.9268 (m-30) cc_final: 0.8981 (m-30) REVERT: O 21 ASP cc_start: 0.7648 (p0) cc_final: 0.7305 (p0) REVERT: O 60 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8448 (mt-10) REVERT: O 69 LYS cc_start: 0.9429 (ttmt) cc_final: 0.9205 (ttpp) REVERT: O 94 THR cc_start: 0.9190 (m) cc_final: 0.8951 (p) REVERT: O 97 MET cc_start: 0.8939 (mmm) cc_final: 0.8607 (mmm) REVERT: O 110 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8583 (mm-30) REVERT: O 116 ARG cc_start: 0.8225 (mmp80) cc_final: 0.7962 (mmp80) REVERT: a 1 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8736 (tmm) REVERT: a 75 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8074 (mmmt) REVERT: a 103 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: a 112 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8812 (mm-30) REVERT: b 91 VAL cc_start: 0.9522 (t) cc_final: 0.9260 (p) REVERT: c 3 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7274 (ttp80) REVERT: c 5 LYS cc_start: 0.9107 (tppt) cc_final: 0.8843 (tppt) REVERT: c 58 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7573 (p0) REVERT: c 69 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8643 (p) REVERT: c 109 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8418 (m110) REVERT: c 114 TYR cc_start: 0.8902 (t80) cc_final: 0.8577 (t80) REVERT: c 117 ASP cc_start: 0.8994 (m-30) cc_final: 0.8654 (p0) REVERT: d 18 ASN cc_start: 0.8984 (p0) cc_final: 0.8725 (p0) REVERT: d 29 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8702 (p) REVERT: d 50 GLU cc_start: 0.7696 (tp30) cc_final: 0.7423 (tp30) REVERT: d 54 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8738 (m-40) REVERT: d 97 ILE cc_start: 0.5912 (OUTLIER) cc_final: 0.5687 (mp) REVERT: e 30 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.6979 (p90) REVERT: f 3 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7944 (ttp-110) REVERT: f 109 ASN cc_start: 0.8875 (m110) cc_final: 0.8599 (m-40) REVERT: f 113 ASP cc_start: 0.9255 (m-30) cc_final: 0.8683 (p0) REVERT: g 48 ASN cc_start: 0.9123 (t0) cc_final: 0.8871 (t0) REVERT: g 86 ASP cc_start: 0.8855 (m-30) cc_final: 0.8562 (t70) REVERT: h 1 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.5777 (tmm) REVERT: h 12 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8057 (p0) REVERT: i 1 MET cc_start: 0.6756 (ttm) cc_final: 0.6480 (ttm) REVERT: j 1 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.5448 (ttt) REVERT: j 12 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8147 (p0) REVERT: j 47 GLN cc_start: 0.9397 (pp30) cc_final: 0.9033 (pp30) REVERT: j 48 ASN cc_start: 0.9109 (t0) cc_final: 0.8702 (t0) REVERT: j 50 GLU cc_start: 0.8433 (pm20) cc_final: 0.7462 (pm20) REVERT: j 75 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8983 (mmmm) REVERT: j 101 ASP cc_start: 0.8327 (p0) cc_final: 0.7926 (p0) REVERT: k 5 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: l 12 ASP cc_start: 0.8375 (p0) cc_final: 0.8132 (p0) REVERT: l 46 ASP cc_start: 0.8620 (p0) cc_final: 0.8150 (p0) REVERT: l 48 ASN cc_start: 0.9399 (m-40) cc_final: 0.8713 (p0) REVERT: l 109 ASN cc_start: 0.9289 (m-40) cc_final: 0.8598 (p0) REVERT: m 2 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.5049 (mtp180) REVERT: m 12 ASP cc_start: 0.7873 (p0) cc_final: 0.7338 (p0) REVERT: m 13 ASP cc_start: 0.7827 (m-30) cc_final: 0.7509 (m-30) REVERT: m 29 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8058 (p) REVERT: m 48 ASN cc_start: 0.9167 (t0) cc_final: 0.8664 (t0) REVERT: m 74 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8239 (tptp) REVERT: n 111 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9174 (pp) REVERT: o 14 GLN cc_start: 0.9403 (mp10) cc_final: 0.9101 (mm-40) REVERT: o 50 GLU cc_start: 0.7559 (tp30) cc_final: 0.7051 (tp30) REVERT: o 54 ASN cc_start: 0.8350 (p0) cc_final: 0.7833 (p0) REVERT: o 65 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6062 (t80) REVERT: o 77 SER cc_start: 0.9334 (p) cc_final: 0.8844 (p) REVERT: o 82 ASP cc_start: 0.8160 (m-30) cc_final: 0.6794 (p0) REVERT: o 103 GLU cc_start: 0.7897 (tp30) cc_final: 0.7620 (tp30) outliers start: 229 outliers final: 171 residues processed: 1272 average time/residue: 0.4548 time to fit residues: 898.9354 Evaluate side-chains 1285 residues out of total 3525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1085 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 112 LYS Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain O residue 18 GLN Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 10 HIS Chi-restraints excluded: chain a residue 13 ASP Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 48 ASN Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 54 ASN Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 86 ASP Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 42 HIS Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 65 TYR Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 106 ASN Chi-restraints excluded: chain i residue 9 ARG Chi-restraints excluded: chain i residue 48 ASN Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 108 LEU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 2 ARG Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 HIS Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 104 TYR Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 10.0000 chunk 316 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 274 optimal weight: 0.0870 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 297 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 ASN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 14 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 47 GLN ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.064645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.050899 restraints weight = 153537.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052482 restraints weight = 93038.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053590 restraints weight = 65411.815| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.321 31470 Z= 0.418 Angle : 1.098 59.193 42780 Z= 0.620 Chirality : 0.052 1.162 4995 Planarity : 0.005 0.095 5565 Dihedral : 7.224 57.914 4227 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 30.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.59 % Favored : 91.25 % Rotamer: Outliers : 6.13 % Allowed : 31.83 % Favored : 62.04 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 3795 helix: 0.16 (0.12), residues: 1612 sheet: -0.15 (0.21), residues: 619 loop : -2.15 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 16 HIS 0.006 0.001 HIS l 42 PHE 0.051 0.002 PHE c 89 TYR 0.077 0.002 TYR O 99 ARG 0.032 0.001 ARG c 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11812.32 seconds wall clock time: 210 minutes 20.03 seconds (12620.03 seconds total)