Starting phenix.real_space_refine on Sun May 12 10:17:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/05_2024/8wp9_37713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/05_2024/8wp9_37713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/05_2024/8wp9_37713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/05_2024/8wp9_37713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/05_2024/8wp9_37713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/05_2024/8wp9_37713.pdb" } resolution = 2.49 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= 0.001 sd= 0.155 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 48 5.16 5 C 13680 2.51 5 N 3528 2.21 5 O 4176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 21432 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "P" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "T" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "U" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "I" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "X" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "D" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "R" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "O" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "C" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "B" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "W" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "K" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "N" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "L" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "M" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "Q" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "J" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "G" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "S" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "V" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Time building chain proxies: 10.56, per 1000 atoms: 0.49 Number of scatterers: 21432 At special positions: 0 Unit cell: (132.581, 132.581, 132.581, 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 48 16.00 O 4176 8.00 N 3528 7.00 C 13680 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: 6.81 Conformation dependent library (CDL) restraints added in 3.7 seconds 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 11.3% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE A 140 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA P 120 " --> pdb=" O GLU P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE P 140 " --> pdb=" O GLU P 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 66 No H-bonds generated for 'chain 'T' and resid 64 through 66' Processing helix chain 'T' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA T 120 " --> pdb=" O GLU T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE T 140 " --> pdb=" O GLU T 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 66 No H-bonds generated for 'chain 'U' and resid 64 through 66' Processing helix chain 'U' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA U 120 " --> pdb=" O GLU U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE U 140 " --> pdb=" O GLU U 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA E 120 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE E 140 " --> pdb=" O GLU E 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA I 120 " --> pdb=" O GLU I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE I 140 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 66 No H-bonds generated for 'chain 'X' and resid 64 through 66' Processing helix chain 'X' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA X 120 " --> pdb=" O GLU X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE X 140 " --> pdb=" O GLU X 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA D 120 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE D 140 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA F 120 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE F 140 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA R 120 " --> pdb=" O GLU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE R 140 " --> pdb=" O GLU R 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 66 No H-bonds generated for 'chain 'O' and resid 64 through 66' Processing helix chain 'O' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA O 120 " --> pdb=" O GLU O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE O 140 " --> pdb=" O GLU O 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA C 120 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE C 140 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE B 140 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 66 No H-bonds generated for 'chain 'W' and resid 64 through 66' Processing helix chain 'W' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA W 120 " --> pdb=" O GLU W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE W 140 " --> pdb=" O GLU W 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 66 No H-bonds generated for 'chain 'K' and resid 64 through 66' Processing helix chain 'K' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA K 120 " --> pdb=" O GLU K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE K 140 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA N 120 " --> pdb=" O GLU N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE N 140 " --> pdb=" O GLU N 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA H 120 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE H 140 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 66 No H-bonds generated for 'chain 'L' and resid 64 through 66' Processing helix chain 'L' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA L 120 " --> pdb=" O GLU L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE L 140 " --> pdb=" O GLU L 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 66 No H-bonds generated for 'chain 'M' and resid 64 through 66' Processing helix chain 'M' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA M 120 " --> pdb=" O GLU M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE M 140 " --> pdb=" O GLU M 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 66 No H-bonds generated for 'chain 'Q' and resid 64 through 66' Processing helix chain 'Q' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA Q 120 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE Q 140 " --> pdb=" O GLU Q 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA J 120 " --> pdb=" O GLU J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE J 140 " --> pdb=" O GLU J 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA G 120 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE G 140 " --> pdb=" O GLU G 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA S 120 " --> pdb=" O GLU S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE S 140 " --> pdb=" O GLU S 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 66 No H-bonds generated for 'chain 'V' and resid 64 through 66' Processing helix chain 'V' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA V 120 " --> pdb=" O GLU V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE V 140 " --> pdb=" O GLU V 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'E' and resid 146 through 147 removed outlier: 7.786A pdb=" N ALA A 122 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 96 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU A 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE C 94 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 97 removed outlier: 5.633A pdb=" N ILE A 94 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU C 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 96 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA C 122 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.944A pdb=" N PHE B 124 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 96 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU B 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE D 94 " --> pdb=" O GLU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 36 through 40 Processing sheet with id=AA7, first strand: chain 'P' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR O 96 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU P 49 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE O 94 " --> pdb=" O GLU P 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE P 94 " --> pdb=" O GLU O 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU O 49 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR P 96 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 142 through 143 Processing sheet with id=AB1, first strand: chain 'P' and resid 146 through 147 removed outlier: 3.829A pdb=" N PHE G 124 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR H 96 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU G 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE H 94 " --> pdb=" O GLU G 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 36 through 40 Processing sheet with id=AB3, first strand: chain 'R' and resid 93 through 97 removed outlier: 5.617A pdb=" N ILE R 94 " --> pdb=" O GLU T 49 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU T 49 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR R 96 " --> pdb=" O ILE T 47 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA T 122 " --> pdb=" O GLU K 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 93 through 97 removed outlier: 5.526A pdb=" N ILE T 94 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU R 49 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR T 96 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 142 through 143 Processing sheet with id=AB6, first strand: chain 'T' and resid 146 through 147 removed outlier: 4.072A pdb=" N PHE X 124 " --> pdb=" O GLU T 147 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR W 96 " --> pdb=" O ILE X 47 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU X 49 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE W 94 " --> pdb=" O GLU X 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 36 through 40 Processing sheet with id=AB8, first strand: chain 'F' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE F 94 " --> pdb=" O GLU U 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU U 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 96 " --> pdb=" O ILE U 47 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA U 122 " --> pdb=" O GLU V 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE U 94 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU F 49 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR U 96 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA F 122 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 142 through 143 Processing sheet with id=AC2, first strand: chain 'U' and resid 146 through 147 removed outlier: 3.712A pdb=" N PHE Q 124 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR S 96 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU Q 49 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE S 94 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 36 through 40 Processing sheet with id=AC4, first strand: chain 'F' and resid 146 through 147 removed outlier: 7.830A pdb=" N ALA E 122 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR N 96 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU E 49 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE N 94 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE E 94 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU N 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR E 96 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 36 through 40 Processing sheet with id=AC7, first strand: chain 'I' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR K 96 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU I 49 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE K 94 " --> pdb=" O GLU I 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE I 94 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU K 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR I 96 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE K 124 " --> pdb=" O GLU O 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 142 through 143 Processing sheet with id=AD1, first strand: chain 'I' and resid 146 through 147 removed outlier: 3.760A pdb=" N PHE J 124 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR L 96 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU J 49 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE L 94 " --> pdb=" O GLU J 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 93 through 97 removed outlier: 5.567A pdb=" N ILE X 94 " --> pdb=" O GLU W 49 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU W 49 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR X 96 " --> pdb=" O ILE W 47 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA W 122 " --> pdb=" O GLU H 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 142 through 143 Processing sheet with id=AD4, first strand: chain 'D' and resid 36 through 40 Processing sheet with id=AD5, first strand: chain 'B' and resid 93 through 97 removed outlier: 5.750A pdb=" N ILE B 94 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU D 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 96 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA D 122 " --> pdb=" O GLU S 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 142 through 143 Processing sheet with id=AD7, first strand: chain 'F' and resid 36 through 40 Processing sheet with id=AD8, first strand: chain 'R' and resid 36 through 40 Processing sheet with id=AD9, first strand: chain 'R' and resid 142 through 143 Processing sheet with id=AE1, first strand: chain 'R' and resid 146 through 147 removed outlier: 4.058A pdb=" N PHE V 124 " --> pdb=" O GLU R 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR M 96 " --> pdb=" O ILE V 47 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU V 49 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE M 94 " --> pdb=" O GLU V 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 142 through 143 Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 40 Processing sheet with id=AE4, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AE5, first strand: chain 'W' and resid 36 through 40 Processing sheet with id=AE6, first strand: chain 'W' and resid 142 through 143 Processing sheet with id=AE7, first strand: chain 'N' and resid 36 through 40 Processing sheet with id=AE8, first strand: chain 'N' and resid 142 through 143 Processing sheet with id=AE9, first strand: chain 'N' and resid 146 through 147 removed outlier: 3.723A pdb=" N PHE M 124 " --> pdb=" O GLU N 147 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR V 96 " --> pdb=" O ILE M 47 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU M 49 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE V 94 " --> pdb=" O GLU M 49 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR G 96 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU H 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE G 94 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 121 through 125 removed outlier: 3.635A pdb=" N TYR J 96 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU L 49 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE J 94 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 93 through 97 removed outlier: 5.581A pdb=" N ILE Q 94 " --> pdb=" O GLU S 49 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU S 49 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2331 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: 7.00 Time building geometry restraints manager: 7.57 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: 6907 1.34 - 1.46: 1738 1.46 - 1.57: 12979 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 21720 Sorted by residual: bond pdb=" CA ILE X 45 " pdb=" CB ILE X 45 " ideal model delta sigma weight residual 1.544 1.570 -0.026 1.42e-02 4.96e+03 3.26e+00 bond pdb=" CA ILE D 45 " pdb=" CB ILE D 45 " ideal model delta sigma weight residual 1.544 1.570 -0.026 1.42e-02 4.96e+03 3.24e+00 bond pdb=" CA ILE T 45 " pdb=" CB ILE T 45 " ideal model delta sigma weight residual 1.544 1.569 -0.025 1.42e-02 4.96e+03 3.21e+00 bond pdb=" CA ILE Q 45 " pdb=" CB ILE Q 45 " ideal model delta sigma weight residual 1.544 1.569 -0.025 1.42e-02 4.96e+03 3.18e+00 bond pdb=" CA ILE L 45 " pdb=" CB ILE L 45 " ideal model delta sigma weight residual 1.544 1.569 -0.025 1.42e-02 4.96e+03 3.17e+00 ... (remaining 21715 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 721 107.34 - 114.00: 12802 114.00 - 120.67: 7801 120.67 - 127.33: 7812 127.33 - 134.00: 168 Bond angle restraints: 29304 Sorted by residual: angle pdb=" CA GLU V 101 " pdb=" CB GLU V 101 " pdb=" CG GLU V 101 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU T 101 " pdb=" CB GLU T 101 " pdb=" CG GLU T 101 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA GLU X 101 " pdb=" CB GLU X 101 " pdb=" CG GLU X 101 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA GLU J 101 " pdb=" CB GLU J 101 " pdb=" CG GLU J 101 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 ... (remaining 29299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 12126 17.73 - 35.45: 1266 35.45 - 53.18: 144 53.18 - 70.91: 24 70.91 - 88.63: 48 Dihedral angle restraints: 13608 sinusoidal: 5688 harmonic: 7920 Sorted by residual: dihedral pdb=" CB GLU I 49 " pdb=" CG GLU I 49 " pdb=" CD GLU I 49 " pdb=" OE1 GLU I 49 " ideal model delta sinusoidal sigma weight residual 0.00 -81.67 81.67 1 3.00e+01 1.11e-03 9.12e+00 dihedral pdb=" CB GLU N 49 " pdb=" CG GLU N 49 " pdb=" CD GLU N 49 " pdb=" OE1 GLU N 49 " ideal model delta sinusoidal sigma weight residual 0.00 -81.67 81.67 1 3.00e+01 1.11e-03 9.12e+00 dihedral pdb=" CB GLU O 49 " pdb=" CG GLU O 49 " pdb=" CD GLU O 49 " pdb=" OE1 GLU O 49 " ideal model delta sinusoidal sigma weight residual 0.00 -81.67 81.67 1 3.00e+01 1.11e-03 9.12e+00 ... (remaining 13605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1506 0.033 - 0.066: 1096 0.066 - 0.099: 410 0.099 - 0.132: 348 0.132 - 0.166: 120 Chirality restraints: 3480 Sorted by residual: chirality pdb=" CA ILE P 35 " pdb=" N ILE P 35 " pdb=" C ILE P 35 " pdb=" CB ILE P 35 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE B 35 " pdb=" N ILE B 35 " pdb=" C ILE B 35 " pdb=" CB ILE B 35 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE G 35 " pdb=" N ILE G 35 " pdb=" C ILE G 35 " pdb=" CB ILE G 35 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 3477 not shown) Planarity restraints: 3720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU W 133 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO W 134 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO W 134 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO W 134 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 133 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO C 134 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 133 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO Q 134 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO Q 134 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO Q 134 " -0.019 5.00e-02 4.00e+02 ... (remaining 3717 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5552 2.83 - 3.35: 15205 3.35 - 3.87: 31265 3.87 - 4.38: 35621 4.38 - 4.90: 67567 Nonbonded interactions: 155210 Sorted by model distance: nonbonded pdb=" OE1 GLU D 78 " pdb=" OG1 THR D 108 " model vdw 2.315 2.440 nonbonded pdb=" OE1 GLU C 78 " pdb=" OG1 THR C 108 " model vdw 2.315 2.440 nonbonded pdb=" OE1 GLU M 78 " pdb=" OG1 THR M 108 " model vdw 2.315 2.440 nonbonded pdb=" OE1 GLU L 78 " pdb=" OG1 THR L 108 " model vdw 2.315 2.440 nonbonded pdb=" OE1 GLU R 78 " pdb=" OG1 THR R 108 " model vdw 2.315 2.440 ... (remaining 155205 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 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: 12.730 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 52.050 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.180 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 0.005 0.043 21720 Z= 0.350 Angle : 0.949 7.239 29304 Z= 0.532 Chirality : 0.061 0.166 3480 Planarity : 0.006 0.034 3720 Dihedral : 15.191 88.632 8472 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.00 % Allowed : 4.00 % Favored : 95.00 % 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: 1.51 (0.16), residues: 2712 helix: None (None), residues: 0 sheet: 3.06 (0.15), residues: 1392 loop : -1.54 (0.12), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP O 59 HIS 0.002 0.001 HIS C 53 PHE 0.005 0.001 PHE R 42 TYR 0.012 0.003 TYR M 106 ARG 0.002 0.001 ARG L 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 807 time to evaluate : 2.613 Fit side-chains revert: symmetry clash REVERT: X 147 GLU cc_start: 0.6990 (pp20) cc_final: 0.6717 (pp20) REVERT: D 98 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7273 (mt-10) REVERT: B 147 GLU cc_start: 0.5987 (pp20) cc_final: 0.5740 (pp20) outliers start: 24 outliers final: 0 residues processed: 824 average time/residue: 1.7070 time to fit residues: 1547.8806 Evaluate side-chains 475 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 119 ASN P 36 GLN P 119 ASN T 36 GLN T 119 ASN T 126 ASN U 36 GLN U 119 ASN E 36 GLN I 36 GLN I 119 ASN X 53 HIS F 53 HIS R 36 GLN O 53 HIS C 36 GLN B 53 HIS W 36 GLN K 36 GLN N 36 GLN N 119 ASN H 36 GLN L 36 GLN L 145 ASN M 36 GLN M 119 ASN Q 53 HIS Q 119 ASN J 36 GLN G 53 HIS S 36 GLN V 36 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 21720 Z= 0.221 Angle : 0.657 8.395 29304 Z= 0.338 Chirality : 0.054 0.147 3480 Planarity : 0.004 0.035 3720 Dihedral : 4.430 14.999 2880 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.88 % Allowed : 20.42 % Favored : 74.71 % 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: 1.99 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.12 (0.15), residues: 1392 loop : -0.89 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 59 HIS 0.008 0.001 HIS O 53 PHE 0.008 0.001 PHE B 124 TYR 0.012 0.002 TYR R 106 ARG 0.004 0.001 ARG L 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 653 time to evaluate : 2.869 Fit side-chains REVERT: A 102 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: T 102 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: T 110 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8579 (tttm) REVERT: E 49 GLU cc_start: 0.7826 (tt0) cc_final: 0.7618 (tt0) REVERT: E 78 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: I 103 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: X 92 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: D 36 GLN cc_start: 0.7955 (mt0) cc_final: 0.7731 (tt0) REVERT: D 78 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: F 118 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: R 118 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: O 118 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: C 78 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: C 118 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: K 49 GLU cc_start: 0.7820 (tt0) cc_final: 0.7618 (tt0) REVERT: K 78 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: N 103 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: L 78 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: J 103 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: V 78 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7717 (tm-30) outliers start: 117 outliers final: 20 residues processed: 719 average time/residue: 1.7696 time to fit residues: 1398.5040 Evaluate side-chains 576 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 539 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 110 LYS Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 87 MET Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 259 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 chunk 238 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN X 53 HIS X 119 ASN D 119 ASN B 53 HIS W 119 ASN K 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 53 HIS Q 119 ASN J 119 ASN G 53 HIS G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 21720 Z= 0.200 Angle : 0.602 8.276 29304 Z= 0.306 Chirality : 0.053 0.145 3480 Planarity : 0.004 0.035 3720 Dihedral : 4.143 13.693 2880 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.29 % Allowed : 22.29 % Favored : 73.42 % 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: 2.23 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.15 (0.15), residues: 1392 loop : -0.54 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 59 HIS 0.006 0.001 HIS G 53 PHE 0.005 0.001 PHE M 124 TYR 0.010 0.002 TYR K 106 ARG 0.002 0.000 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 570 time to evaluate : 2.720 Fit side-chains REVERT: A 102 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: P 102 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: U 102 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: E 78 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: E 102 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6967 (mt-10) REVERT: E 104 GLU cc_start: 0.7407 (tp30) cc_final: 0.7078 (mm-30) REVERT: E 106 TYR cc_start: 0.8429 (p90) cc_final: 0.8209 (p90) REVERT: X 92 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: F 78 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: F 118 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: R 78 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: R 118 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: O 78 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: O 118 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: C 78 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: C 118 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: W 78 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: K 78 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: K 102 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: K 104 GLU cc_start: 0.7393 (tp30) cc_final: 0.7067 (mm-30) REVERT: H 49 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: H 78 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: L 78 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: L 102 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: L 103 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: L 106 TYR cc_start: 0.8446 (p90) cc_final: 0.8203 (p90) REVERT: M 110 LYS cc_start: 0.8827 (tttm) cc_final: 0.8577 (tttm) REVERT: J 78 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: J 101 GLU cc_start: 0.7405 (mp0) cc_final: 0.7175 (mm-30) REVERT: S 78 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: V 78 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: V 102 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: V 106 TYR cc_start: 0.8446 (p90) cc_final: 0.8174 (p90) outliers start: 103 outliers final: 30 residues processed: 634 average time/residue: 1.7858 time to fit residues: 1244.4885 Evaluate side-chains 595 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 539 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 255 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.7667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 21720 Z= 0.313 Angle : 0.689 8.954 29304 Z= 0.348 Chirality : 0.054 0.149 3480 Planarity : 0.004 0.036 3720 Dihedral : 4.505 13.522 2880 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 5.33 % Allowed : 21.29 % Favored : 73.38 % 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: 2.18 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.15 (0.15), residues: 1392 loop : -0.61 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE M 124 TYR 0.008 0.002 TYR E 106 ARG 0.004 0.001 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 579 time to evaluate : 2.629 Fit side-chains REVERT: A 78 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: P 78 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: T 78 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: U 78 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: E 102 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: E 104 GLU cc_start: 0.7412 (tp30) cc_final: 0.7123 (mm-30) REVERT: I 78 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: I 102 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: X 78 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: X 92 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: D 78 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: D 91 SER cc_start: 0.5832 (OUTLIER) cc_final: 0.5534 (t) REVERT: F 78 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: F 118 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: R 78 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: R 118 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: O 78 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: O 118 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: C 78 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: C 118 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: W 78 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: K 102 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: K 104 GLU cc_start: 0.7407 (tp30) cc_final: 0.7123 (mm-30) REVERT: N 78 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: N 102 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: H 78 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: H 91 SER cc_start: 0.5899 (OUTLIER) cc_final: 0.5663 (t) REVERT: L 78 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: L 102 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: L 103 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: M 78 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: M 110 LYS cc_start: 0.8852 (tttm) cc_final: 0.8560 (tttm) REVERT: Q 78 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: J 78 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: J 102 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: S 78 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: V 78 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: V 102 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7332 (mt-10) outliers start: 128 outliers final: 49 residues processed: 663 average time/residue: 1.7567 time to fit residues: 1280.2642 Evaluate side-chains 635 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 551 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 78 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 190 optimal weight: 0.0470 chunk 105 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.7725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 21720 Z= 0.261 Angle : 0.638 8.680 29304 Z= 0.321 Chirality : 0.053 0.146 3480 Planarity : 0.004 0.032 3720 Dihedral : 4.307 12.771 2880 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.88 % Allowed : 22.58 % Favored : 72.54 % 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: 2.21 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.12 (0.15), residues: 1392 loop : -0.55 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE M 124 TYR 0.005 0.001 TYR E 96 ARG 0.003 0.000 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 564 time to evaluate : 2.732 Fit side-chains REVERT: A 78 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: P 78 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: T 78 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: U 78 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: E 78 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: E 102 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: E 104 GLU cc_start: 0.7383 (tp30) cc_final: 0.7171 (mm-30) REVERT: I 102 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: X 78 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: X 92 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: D 78 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: D 91 SER cc_start: 0.5778 (OUTLIER) cc_final: 0.5497 (t) REVERT: F 78 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: F 118 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: R 78 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: R 118 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: O 78 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: O 118 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: C 78 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: C 118 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: W 78 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: K 78 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: K 102 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: K 104 GLU cc_start: 0.7374 (tp30) cc_final: 0.7161 (mm-30) REVERT: N 102 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: H 78 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: H 91 SER cc_start: 0.5850 (OUTLIER) cc_final: 0.5583 (t) REVERT: L 78 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: L 103 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: M 78 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: M 110 LYS cc_start: 0.8854 (tttm) cc_final: 0.8560 (tttm) REVERT: Q 78 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: J 78 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: J 102 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: S 78 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: S 91 SER cc_start: 0.5838 (OUTLIER) cc_final: 0.5637 (t) REVERT: V 78 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: V 102 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7295 (mt-10) outliers start: 117 outliers final: 50 residues processed: 648 average time/residue: 1.7279 time to fit residues: 1233.7873 Evaluate side-chains 640 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 555 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 255 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21720 Z= 0.156 Angle : 0.543 7.993 29304 Z= 0.273 Chirality : 0.052 0.141 3480 Planarity : 0.003 0.024 3720 Dihedral : 3.855 12.427 2880 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.33 % Allowed : 23.62 % Favored : 72.04 % 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: 2.38 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.16 (0.15), residues: 1392 loop : -0.32 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP O 59 HIS 0.002 0.000 HIS T 53 PHE 0.005 0.001 PHE M 124 TYR 0.010 0.002 TYR V 106 ARG 0.002 0.000 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 559 time to evaluate : 2.776 Fit side-chains REVERT: A 78 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: P 78 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: U 78 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: E 78 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: E 102 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: E 110 LYS cc_start: 0.8842 (tttm) cc_final: 0.8592 (tttm) REVERT: I 78 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: X 78 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: D 78 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: D 91 SER cc_start: 0.5773 (OUTLIER) cc_final: 0.5498 (t) REVERT: F 78 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: F 118 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: R 78 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: R 118 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: O 78 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: O 118 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: C 118 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: W 78 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: K 78 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: K 102 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: K 110 LYS cc_start: 0.8836 (tttm) cc_final: 0.8566 (tttm) REVERT: N 78 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: H 78 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: H 91 SER cc_start: 0.5801 (OUTLIER) cc_final: 0.5541 (t) REVERT: L 103 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: L 110 LYS cc_start: 0.8847 (tttm) cc_final: 0.8592 (tttm) REVERT: M 78 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: M 102 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: M 110 LYS cc_start: 0.8859 (tttm) cc_final: 0.8573 (tttm) REVERT: Q 78 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: J 102 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: J 110 LYS cc_start: 0.8846 (tttm) cc_final: 0.8552 (tttm) REVERT: S 78 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: S 102 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: V 110 LYS cc_start: 0.8848 (tttm) cc_final: 0.8597 (tttm) outliers start: 104 outliers final: 47 residues processed: 635 average time/residue: 1.7099 time to fit residues: 1197.8975 Evaluate side-chains 625 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 549 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 78 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 21720 Z= 0.335 Angle : 0.691 9.114 29304 Z= 0.349 Chirality : 0.054 0.149 3480 Planarity : 0.004 0.040 3720 Dihedral : 4.425 12.932 2880 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.83 % Allowed : 23.62 % Favored : 71.54 % 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: 2.20 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.05 (0.15), residues: 1392 loop : -0.46 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 59 HIS 0.002 0.001 HIS T 53 PHE 0.008 0.001 PHE M 124 TYR 0.008 0.002 TYR K 106 ARG 0.004 0.001 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 564 time to evaluate : 2.568 Fit side-chains REVERT: A 37 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8764 (mm) REVERT: A 78 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: P 78 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: T 78 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: U 78 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: E 78 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: I 78 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: X 78 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: D 78 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: D 91 SER cc_start: 0.5733 (OUTLIER) cc_final: 0.5476 (t) REVERT: F 78 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: F 118 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: R 78 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: R 118 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: O 78 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: O 118 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: C 78 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: C 118 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: W 78 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: W 91 SER cc_start: 0.5782 (OUTLIER) cc_final: 0.5529 (t) REVERT: W 102 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: K 78 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: N 78 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: H 78 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: H 91 SER cc_start: 0.5771 (OUTLIER) cc_final: 0.5530 (t) REVERT: L 78 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: M 78 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: M 102 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: Q 78 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: J 78 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: J 102 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: S 78 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7710 (tm-30) outliers start: 116 outliers final: 58 residues processed: 646 average time/residue: 1.7042 time to fit residues: 1214.6300 Evaluate side-chains 650 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 560 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 78 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21720 Z= 0.135 Angle : 0.519 7.959 29304 Z= 0.261 Chirality : 0.051 0.141 3480 Planarity : 0.003 0.023 3720 Dihedral : 3.731 12.350 2880 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.25 % Allowed : 25.83 % Favored : 70.92 % 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: 2.47 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.14 (0.15), residues: 1392 loop : -0.15 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP S 59 HIS 0.002 0.000 HIS T 53 PHE 0.004 0.001 PHE M 124 TYR 0.008 0.001 TYR B 106 ARG 0.001 0.000 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 542 time to evaluate : 3.032 Fit side-chains REVERT: P 78 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: T 78 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: U 78 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: E 78 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: E 110 LYS cc_start: 0.8845 (tttm) cc_final: 0.8586 (tttm) REVERT: I 78 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: I 102 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: X 78 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: D 78 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: D 91 SER cc_start: 0.5759 (OUTLIER) cc_final: 0.5495 (t) REVERT: F 78 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: F 118 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: R 78 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: R 118 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: O 78 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: O 118 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: C 78 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: C 110 LYS cc_start: 0.8805 (tttm) cc_final: 0.8515 (tttm) REVERT: C 118 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: W 78 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: W 91 SER cc_start: 0.5763 (OUTLIER) cc_final: 0.5503 (t) REVERT: K 78 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: K 110 LYS cc_start: 0.8833 (tttm) cc_final: 0.8546 (tttm) REVERT: N 78 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: N 102 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: H 78 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: H 91 SER cc_start: 0.5750 (OUTLIER) cc_final: 0.5518 (t) REVERT: L 110 LYS cc_start: 0.8846 (tttm) cc_final: 0.8584 (tttm) REVERT: M 78 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: M 102 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: M 110 LYS cc_start: 0.8863 (tttm) cc_final: 0.8602 (tttm) REVERT: Q 78 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: J 78 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: J 110 LYS cc_start: 0.8846 (tttm) cc_final: 0.8583 (tttm) REVERT: S 78 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: V 78 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: V 110 LYS cc_start: 0.8856 (tttm) cc_final: 0.8599 (tttm) outliers start: 78 outliers final: 38 residues processed: 603 average time/residue: 1.7036 time to fit residues: 1135.7344 Evaluate side-chains 605 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 537 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain N residue 78 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 5.9990 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 0.0040 chunk 214 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.7715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 21720 Z= 0.147 Angle : 0.528 7.876 29304 Z= 0.265 Chirality : 0.051 0.141 3480 Planarity : 0.003 0.024 3720 Dihedral : 3.702 12.331 2880 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.08 % Allowed : 26.83 % Favored : 70.08 % 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: 2.55 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.15 (0.15), residues: 1392 loop : -0.05 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 59 HIS 0.002 0.000 HIS T 53 PHE 0.005 0.001 PHE M 124 TYR 0.012 0.002 TYR S 106 ARG 0.001 0.000 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 538 time to evaluate : 2.571 Fit side-chains REVERT: P 78 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: T 78 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: U 78 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: E 78 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: E 110 LYS cc_start: 0.8845 (tttm) cc_final: 0.8590 (tttm) REVERT: I 78 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: I 102 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: X 78 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: D 78 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: D 91 SER cc_start: 0.5761 (OUTLIER) cc_final: 0.5506 (t) REVERT: F 78 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: F 110 LYS cc_start: 0.8824 (tttm) cc_final: 0.8527 (tttm) REVERT: F 118 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: R 78 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: R 110 LYS cc_start: 0.8815 (tttm) cc_final: 0.8526 (tttm) REVERT: R 118 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: O 78 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: O 110 LYS cc_start: 0.8826 (tttm) cc_final: 0.8533 (tttm) REVERT: O 118 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: C 78 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: C 110 LYS cc_start: 0.8803 (tttm) cc_final: 0.8515 (tttm) REVERT: C 118 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: W 78 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: W 91 SER cc_start: 0.5724 (OUTLIER) cc_final: 0.5458 (t) REVERT: K 78 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: K 110 LYS cc_start: 0.8846 (tttm) cc_final: 0.8564 (tttm) REVERT: N 78 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: N 102 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: H 78 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: H 91 SER cc_start: 0.5772 (OUTLIER) cc_final: 0.5529 (t) REVERT: L 110 LYS cc_start: 0.8852 (tttm) cc_final: 0.8596 (tttm) REVERT: M 78 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: M 102 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: M 110 LYS cc_start: 0.8858 (tttm) cc_final: 0.8603 (tttm) REVERT: Q 78 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: J 78 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: J 102 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: J 110 LYS cc_start: 0.8850 (tttm) cc_final: 0.8591 (tttm) REVERT: S 78 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: V 78 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: V 110 LYS cc_start: 0.8856 (tttm) cc_final: 0.8603 (tttm) outliers start: 74 outliers final: 49 residues processed: 598 average time/residue: 1.7115 time to fit residues: 1133.1059 Evaluate side-chains 613 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 533 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 78 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 145 ASN Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 263 optimal weight: 0.5980 chunk 242 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.7802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 21720 Z= 0.224 Angle : 0.603 8.452 29304 Z= 0.302 Chirality : 0.052 0.145 3480 Planarity : 0.003 0.031 3720 Dihedral : 4.023 12.679 2880 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.62 % Allowed : 27.12 % Favored : 69.25 % 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: 2.40 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.08 (0.15), residues: 1392 loop : -0.18 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 59 HIS 0.002 0.001 HIS T 53 PHE 0.006 0.001 PHE M 124 TYR 0.004 0.001 TYR E 96 ARG 0.002 0.000 ARG H 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 560 time to evaluate : 2.721 Fit side-chains REVERT: A 78 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: P 78 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: T 78 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: U 78 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: E 78 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: E 110 LYS cc_start: 0.8862 (tttm) cc_final: 0.8600 (tttm) REVERT: I 78 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: I 102 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: X 78 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: D 78 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: D 91 SER cc_start: 0.5739 (OUTLIER) cc_final: 0.5497 (t) REVERT: F 78 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: F 118 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: R 78 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: R 118 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: O 78 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: O 118 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: C 78 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: C 118 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: W 78 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: W 91 SER cc_start: 0.5700 (OUTLIER) cc_final: 0.5454 (t) REVERT: K 78 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: K 110 LYS cc_start: 0.8852 (tttm) cc_final: 0.8556 (tttm) REVERT: N 78 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: N 102 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: H 78 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: H 91 SER cc_start: 0.5754 (OUTLIER) cc_final: 0.5524 (t) REVERT: H 102 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: L 78 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: L 110 LYS cc_start: 0.8860 (tttm) cc_final: 0.8600 (tttm) REVERT: M 78 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: M 102 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: M 110 LYS cc_start: 0.8853 (tttm) cc_final: 0.8590 (tttm) REVERT: Q 78 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: J 78 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: J 102 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: J 110 LYS cc_start: 0.8849 (tttm) cc_final: 0.8585 (tttm) REVERT: S 78 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: V 78 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: V 110 LYS cc_start: 0.8866 (tttm) cc_final: 0.8608 (tttm) outliers start: 87 outliers final: 50 residues processed: 625 average time/residue: 1.7187 time to fit residues: 1183.0456 Evaluate side-chains 643 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 559 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 78 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 193 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120710 restraints weight = 25575.981| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.36 r_work: 0.3460 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.7735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 21720 Z= 0.159 Angle : 0.545 8.110 29304 Z= 0.273 Chirality : 0.052 0.143 3480 Planarity : 0.003 0.024 3720 Dihedral : 3.767 12.395 2880 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.38 % Allowed : 27.38 % Favored : 69.25 % 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: 2.50 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.04 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP S 59 HIS 0.002 0.000 HIS T 53 PHE 0.005 0.001 PHE J 124 TYR 0.010 0.002 TYR P 106 ARG 0.001 0.000 ARG H 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16195.28 seconds wall clock time: 286 minutes 28.41 seconds (17188.41 seconds total)