Starting phenix.real_space_refine on Sun Feb 18 18:12:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1k_0590/02_2024/6o1k_0590_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1k_0590/02_2024/6o1k_0590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1k_0590/02_2024/6o1k_0590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1k_0590/02_2024/6o1k_0590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1k_0590/02_2024/6o1k_0590_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1k_0590/02_2024/6o1k_0590_neut.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 34 5.49 5 S 30 5.16 5 C 7194 2.51 5 N 2033 2.21 5 O 2139 1.98 5 H 11277 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 230": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 230": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 239": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22707 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "B" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "C" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "D" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "E" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "F" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "G" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1100 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "H" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "I" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "J" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "K" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "L" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1095 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain: "M" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "N" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1100 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "O" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Classifications: {'RNA': 18} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 17} Chain: "P" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Classifications: {'RNA': 18} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 17} Time building chain proxies: 10.44, per 1000 atoms: 0.46 Number of scatterers: 22707 At special positions: 0 Unit cell: (97.01, 123.17, 79.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 34 15.00 O 2139 8.00 N 2033 7.00 C 7194 6.00 H 11277 1.00 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: 17.32 Conformation dependent library (CDL) restraints added in 2.2 seconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 22.5% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.68 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 18 through 25 removed outlier: 3.612A pdb=" N GLN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.708A pdb=" N ASP A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.602A pdb=" N GLN B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.751A pdb=" N ASP B 45 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.710A pdb=" N GLU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.897A pdb=" N ARG B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.678A pdb=" N GLU C 18 " --> pdb=" O THR C 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 18 removed outlier: 3.694A pdb=" N TYR D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 18 removed outlier: 3.783A pdb=" N TYR E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 18 Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.565A pdb=" N TYR G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 18 removed outlier: 3.503A pdb=" N THR H 14 " --> pdb=" O PRO H 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 18 removed outlier: 3.551A pdb=" N TYR I 11 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU I 18 " --> pdb=" O THR I 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 18 removed outlier: 3.920A pdb=" N GLU J 18 " --> pdb=" O THR J 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 19 removed outlier: 3.639A pdb=" N THR K 14 " --> pdb=" O PRO K 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 18 removed outlier: 3.504A pdb=" N TYR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU L 12 " --> pdb=" O GLN L 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 18 removed outlier: 3.793A pdb=" N TYR M 11 " --> pdb=" O LEU M 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 17 removed outlier: 3.574A pdb=" N TYR N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 removed outlier: 6.877A pdb=" N ARG A 2 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N CYS A 32 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 4 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLN A 34 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL A 6 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.846A pdb=" N SER A 103 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N CYS A 146 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A 105 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N SER A 148 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 107 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 58 removed outlier: 6.804A pdb=" N ARG B 2 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N CYS B 32 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 4 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN B 34 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE B 250 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA B 235 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 252 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 81 Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 64 removed outlier: 7.283A pdb=" N LEU C 45 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N PHE C 39 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL C 43 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER D 60 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 61 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE D 36 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS D 47 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER D 38 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER E 60 " --> pdb=" O TYR D 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.663A pdb=" N SER F 60 " --> pdb=" O TYR E 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 39 removed outlier: 6.492A pdb=" N LEU F 45 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE F 39 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER F 51 " --> pdb=" O PRO H 64 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER H 60 " --> pdb=" O TYR F 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 31 through 34 removed outlier: 6.681A pdb=" N SER G 60 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET H 53 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER H 51 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL H 43 " --> pdb=" O PHE H 39 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE H 39 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU H 45 " --> pdb=" O GLU H 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.991A pdb=" N SER G 38 " --> pdb=" O LEU G 45 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 31 through 34 removed outlier: 6.883A pdb=" N SER I 60 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL N 43 " --> pdb=" O PHE N 39 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE N 39 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU N 45 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER N 60 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET M 53 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER M 51 " --> pdb=" O PRO N 64 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL M 43 " --> pdb=" O PHE M 39 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE M 39 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU M 45 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 43 through 46 removed outlier: 6.898A pdb=" N SER J 60 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN J 35 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU J 45 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE J 39 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL J 43 " --> pdb=" O PHE J 39 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER J 51 " --> pdb=" O PRO K 64 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER K 60 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU K 45 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE K 39 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL K 43 " --> pdb=" O PHE K 39 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER K 51 " --> pdb=" O PRO L 64 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER L 60 " --> pdb=" O TYR K 55 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR L 25 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL L 62 " --> pdb=" O SER L 23 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER L 23 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN L 35 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU L 45 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE L 39 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL L 43 " --> pdb=" O PHE L 39 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER L 51 " --> pdb=" O PRO M 64 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER M 60 " --> pdb=" O TYR L 55 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1134 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: 8.15 Time building geometry restraints manager: 18.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.08: 3269 1.08 - 1.26: 9715 1.26 - 1.45: 3405 1.45 - 1.63: 6597 1.63 - 1.81: 52 Bond restraints: 23038 Sorted by residual: bond pdb=" C2 A P 3 " pdb=" H2 A P 3 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 PHE B 41 " pdb=" HD2 PHE B 41 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C8 A P 16 " pdb=" H8 A P 16 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN K 48 " pdb="HD21 ASN K 48 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CZ2 TRP B 203 " pdb=" HZ2 TRP B 203 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 23033 not shown) Histogram of bond angle deviations from ideal: 90.18 - 102.01: 64 102.01 - 113.84: 27439 113.84 - 125.67: 13685 125.67 - 137.50: 494 137.50 - 149.33: 2 Bond angle restraints: 41684 Sorted by residual: angle pdb=" C6 A O 14 " pdb=" N6 A O 14 " pdb=" H61 A O 14 " ideal model delta sigma weight residual 120.00 90.18 29.82 3.00e+00 1.11e-01 9.88e+01 angle pdb=" C6 A O 11 " pdb=" N6 A O 11 " pdb=" H61 A O 11 " ideal model delta sigma weight residual 120.00 149.33 -29.33 3.00e+00 1.11e-01 9.56e+01 angle pdb=" C ARG H 69 " pdb=" N LEU H 70 " pdb=" CA LEU H 70 " ideal model delta sigma weight residual 120.68 131.97 -11.29 1.52e+00 4.33e-01 5.52e+01 angle pdb=" C6 A P 2 " pdb=" N6 A P 2 " pdb=" H61 A P 2 " ideal model delta sigma weight residual 120.00 140.57 -20.57 3.00e+00 1.11e-01 4.70e+01 angle pdb=" C6 A P 10 " pdb=" N6 A P 10 " pdb=" H61 A P 10 " ideal model delta sigma weight residual 120.00 100.62 19.38 3.00e+00 1.11e-01 4.18e+01 ... (remaining 41679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 9750 17.64 - 35.28: 488 35.28 - 52.92: 205 52.92 - 70.57: 278 70.57 - 88.21: 35 Dihedral angle restraints: 10756 sinusoidal: 6214 harmonic: 4542 Sorted by residual: dihedral pdb=" CA VAL G 50 " pdb=" C VAL G 50 " pdb=" N SER G 51 " pdb=" CA SER G 51 " ideal model delta harmonic sigma weight residual -180.00 -129.61 -50.39 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ASP H 9 " pdb=" C ASP H 9 " pdb=" N PRO H 10 " pdb=" CA PRO H 10 " ideal model delta harmonic sigma weight residual 180.00 135.43 44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA GLN G 52 " pdb=" C GLN G 52 " pdb=" N MET G 53 " pdb=" CA MET G 53 " ideal model delta harmonic sigma weight residual 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 10753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1403 0.066 - 0.131: 344 0.131 - 0.197: 74 0.197 - 0.263: 19 0.263 - 0.328: 5 Chirality restraints: 1845 Sorted by residual: chirality pdb=" CA ASP A 199 " pdb=" N ASP A 199 " pdb=" C ASP A 199 " pdb=" CB ASP A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB ILE N 24 " pdb=" CA ILE N 24 " pdb=" CG1 ILE N 24 " pdb=" CG2 ILE N 24 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PRO B 226 " pdb=" N PRO B 226 " pdb=" C PRO B 226 " pdb=" CB PRO B 226 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1842 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 255 " -0.216 2.00e-02 2.50e+03 9.37e-02 3.51e+02 pdb=" CG TRP B 255 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 255 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 255 " 0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP B 255 " 0.091 2.00e-02 2.50e+03 pdb=" CE2 TRP B 255 " 0.034 2.00e-02 2.50e+03 pdb=" CE3 TRP B 255 " 0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 255 " -0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 255 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP B 255 " -0.047 2.00e-02 2.50e+03 pdb=" HD1 TRP B 255 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 TRP B 255 " 0.151 2.00e-02 2.50e+03 pdb=" HE3 TRP B 255 " 0.125 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 255 " -0.101 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 255 " 0.033 2.00e-02 2.50e+03 pdb=" HH2 TRP B 255 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 A O 5 " 0.079 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" N6 A O 5 " -0.319 2.00e-02 2.50e+03 pdb=" H61 A O 5 " 0.119 2.00e-02 2.50e+03 pdb=" H62 A O 5 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 A O 1 " 0.074 2.00e-02 2.50e+03 1.68e-01 2.81e+02 pdb=" N6 A O 1 " -0.289 2.00e-02 2.50e+03 pdb=" H61 A O 1 " 0.107 2.00e-02 2.50e+03 pdb=" H62 A O 1 " 0.108 2.00e-02 2.50e+03 ... (remaining 3182 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.79: 221 1.79 - 2.49: 14413 2.49 - 3.20: 69486 3.20 - 3.90: 95111 3.90 - 4.60: 145176 Nonbonded interactions: 324407 Sorted by model distance: nonbonded pdb=" HG SER E 38 " pdb=" H PHE E 39 " model vdw 1.091 2.100 nonbonded pdb=" HG SER J 60 " pdb=" H THR J 61 " model vdw 1.251 2.100 nonbonded pdb=" HG SER C 60 " pdb=" H THR C 61 " model vdw 1.270 2.100 nonbonded pdb=" HG SER M 60 " pdb=" H THR M 61 " model vdw 1.273 2.100 nonbonded pdb=" HD2 TYR K 55 " pdb=" HE2 HIS K 57 " model vdw 1.317 2.100 ... (remaining 324402 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' } ncs_group { reference = (chain 'C' and resid 6 through 69) selection = (chain 'D' and resid 6 through 69) selection = (chain 'E' and resid 6 through 69) selection = (chain 'F' and resid 6 through 69) selection = (chain 'G' and resid 6 through 69) selection = (chain 'H' and resid 6 through 69) selection = (chain 'I' and resid 6 through 69) selection = (chain 'J' and resid 6 through 69) selection = (chain 'K' and resid 6 through 69) selection = (chain 'L' and resid 6 through 69) selection = (chain 'M' and resid 6 through 69) selection = (chain 'N' and resid 6 through 69) } ncs_group { reference = chain 'O' selection = chain 'P' } 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: 0.010 Normalize map: mean=0, sd=1: 0.410 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: 0.330 Extract box with map and model: 2.850 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 78.650 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 : 0.006 0.049 11761 Z= 0.360 Angle : 1.060 12.333 16127 Z= 0.633 Chirality : 0.064 0.328 1845 Planarity : 0.011 0.182 1926 Dihedral : 12.092 81.045 4597 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 0.17 % Allowed : 4.92 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -3.06 (0.21), residues: 1289 helix: -3.47 (0.19), residues: 251 sheet: -2.01 (0.21), residues: 464 loop : -1.08 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.132 0.015 TRP B 255 HIS 0.013 0.003 HIS A 153 PHE 0.050 0.005 PHE A 243 TYR 0.065 0.004 TYR A 143 ARG 0.015 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 396 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.7998 (p0) cc_final: 0.7528 (p0) REVERT: A 41 PHE cc_start: 0.7926 (t80) cc_final: 0.7709 (t80) REVERT: A 135 LYS cc_start: 0.8423 (mtmt) cc_final: 0.7800 (tptp) REVERT: A 139 LYS cc_start: 0.8814 (mttt) cc_final: 0.8581 (mttm) REVERT: B 134 SER cc_start: 0.9138 (t) cc_final: 0.8912 (p) REVERT: B 135 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7845 (tptt) REVERT: B 211 GLU cc_start: 0.7244 (pp20) cc_final: 0.7027 (pp20) REVERT: B 234 ASN cc_start: 0.7787 (m-40) cc_final: 0.7502 (t0) REVERT: D 51 SER cc_start: 0.8341 (m) cc_final: 0.7993 (t) REVERT: E 35 GLN cc_start: 0.7801 (mp10) cc_final: 0.7076 (mp10) REVERT: E 55 TYR cc_start: 0.8731 (m-80) cc_final: 0.8358 (m-80) REVERT: F 17 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7835 (mmmt) REVERT: F 37 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7514 (mt-10) REVERT: F 45 LEU cc_start: 0.8016 (mp) cc_final: 0.7483 (tt) REVERT: G 17 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8228 (mtmt) REVERT: G 35 GLN cc_start: 0.8402 (mt0) cc_final: 0.8052 (mt0) REVERT: G 47 LYS cc_start: 0.8304 (tmtp) cc_final: 0.7958 (tttp) REVERT: H 40 ASP cc_start: 0.7886 (m-30) cc_final: 0.7611 (m-30) REVERT: J 36 ILE cc_start: 0.9178 (tt) cc_final: 0.8834 (mp) REVERT: L 68 VAL cc_start: 0.6985 (t) cc_final: 0.6643 (p) REVERT: M 47 LYS cc_start: 0.8565 (ttpm) cc_final: 0.8311 (ttpt) outliers start: 2 outliers final: 2 residues processed: 397 average time/residue: 0.6828 time to fit residues: 359.7491 Evaluate side-chains 263 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain I residue 9 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 184 ASN B 7 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS B 136 GLN B 214 ASN E 8 GLN E 33 GLN F 13 ASN H 48 ASN I 33 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 ASN J 52 GLN K 8 GLN K 48 ASN L 48 ASN L 52 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11761 Z= 0.184 Angle : 0.587 7.873 16127 Z= 0.301 Chirality : 0.046 0.155 1845 Planarity : 0.006 0.095 1926 Dihedral : 11.058 73.678 1939 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 1.33 % Allowed : 9.34 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -1.63 (0.23), residues: 1289 helix: -1.22 (0.30), residues: 263 sheet: -1.58 (0.22), residues: 461 loop : -0.27 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 217 HIS 0.006 0.001 HIS K 57 PHE 0.010 0.001 PHE F 39 TYR 0.010 0.001 TYR K 55 ARG 0.006 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 285 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7955 (t80) cc_final: 0.7679 (t80) REVERT: A 135 LYS cc_start: 0.8451 (mtmt) cc_final: 0.7820 (tptp) REVERT: A 139 LYS cc_start: 0.8867 (mttt) cc_final: 0.8603 (mttm) REVERT: B 35 ASP cc_start: 0.8059 (t70) cc_final: 0.7854 (t0) REVERT: B 61 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7190 (mt-10) REVERT: B 134 SER cc_start: 0.9162 (t) cc_final: 0.8833 (p) REVERT: B 135 LYS cc_start: 0.8420 (mtmt) cc_final: 0.7700 (tptp) REVERT: E 35 GLN cc_start: 0.7794 (mp10) cc_final: 0.7135 (mp10) REVERT: F 17 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7655 (mmmt) REVERT: G 35 GLN cc_start: 0.8483 (mt0) cc_final: 0.8131 (mt0) REVERT: H 40 ASP cc_start: 0.7645 (m-30) cc_final: 0.7422 (m-30) REVERT: I 19 ARG cc_start: 0.7030 (mtt90) cc_final: 0.6721 (mmt-90) REVERT: J 31 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7809 (ptmt) REVERT: J 36 ILE cc_start: 0.9164 (tt) cc_final: 0.8707 (mp) REVERT: K 9 ASP cc_start: 0.8350 (m-30) cc_final: 0.7748 (m-30) REVERT: L 66 ARG cc_start: 0.8263 (ptt90) cc_final: 0.7991 (ptt90) REVERT: M 9 ASP cc_start: 0.8256 (m-30) cc_final: 0.8023 (m-30) REVERT: M 41 GLN cc_start: 0.8900 (pp30) cc_final: 0.7948 (pp30) outliers start: 16 outliers final: 11 residues processed: 297 average time/residue: 0.7100 time to fit residues: 279.7233 Evaluate side-chains 252 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 241 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 38 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 57 HIS F 8 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS J 8 GLN L 57 HIS ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11761 Z= 0.259 Angle : 0.572 5.678 16127 Z= 0.295 Chirality : 0.046 0.176 1845 Planarity : 0.005 0.084 1926 Dihedral : 10.779 73.520 1939 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.66 % Rotamer: Outliers : 1.42 % Allowed : 12.26 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -1.05 (0.24), residues: 1289 helix: -0.24 (0.34), residues: 263 sheet: -1.43 (0.23), residues: 459 loop : 0.02 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 217 HIS 0.006 0.002 HIS K 57 PHE 0.013 0.001 PHE A 125 TYR 0.013 0.001 TYR K 55 ARG 0.005 0.001 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 262 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8093 (t80) cc_final: 0.7791 (t80) REVERT: A 124 LYS cc_start: 0.8318 (ttmm) cc_final: 0.7882 (ttmm) REVERT: A 128 ASP cc_start: 0.8590 (m-30) cc_final: 0.8183 (m-30) REVERT: A 135 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7886 (tptp) REVERT: A 139 LYS cc_start: 0.8882 (mttt) cc_final: 0.8587 (mttm) REVERT: B 197 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7164 (mt-10) REVERT: E 35 GLN cc_start: 0.7831 (mp10) cc_final: 0.7138 (mp10) REVERT: G 17 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8098 (mtmm) REVERT: G 35 GLN cc_start: 0.8604 (mt0) cc_final: 0.8263 (mt0) REVERT: G 47 LYS cc_start: 0.8877 (tptt) cc_final: 0.8654 (tptp) REVERT: J 18 GLU cc_start: 0.8131 (pp20) cc_final: 0.7526 (pp20) REVERT: L 66 ARG cc_start: 0.8267 (ptt90) cc_final: 0.7978 (ptt90) REVERT: M 9 ASP cc_start: 0.8178 (m-30) cc_final: 0.7927 (m-30) outliers start: 17 outliers final: 13 residues processed: 274 average time/residue: 0.6784 time to fit residues: 249.0092 Evaluate side-chains 246 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 233 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11761 Z= 0.212 Angle : 0.542 7.283 16127 Z= 0.277 Chirality : 0.045 0.167 1845 Planarity : 0.005 0.069 1926 Dihedral : 10.626 73.659 1939 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.27 % Rotamer: Outliers : 2.17 % Allowed : 12.76 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1289 helix: 0.08 (0.34), residues: 263 sheet: -1.35 (0.23), residues: 457 loop : 0.23 (0.29), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 217 HIS 0.006 0.001 HIS L 57 PHE 0.009 0.001 PHE A 125 TYR 0.013 0.001 TYR K 55 ARG 0.007 0.000 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 249 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8139 (t80) cc_final: 0.7864 (t80) REVERT: A 124 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7950 (ttmm) REVERT: A 128 ASP cc_start: 0.8598 (m-30) cc_final: 0.8213 (m-30) REVERT: A 139 LYS cc_start: 0.8874 (mttt) cc_final: 0.8642 (mttm) REVERT: B 197 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7195 (mt-10) REVERT: E 18 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7197 (tm-30) REVERT: E 35 GLN cc_start: 0.7808 (mp10) cc_final: 0.7146 (mp10) REVERT: G 35 GLN cc_start: 0.8591 (mt0) cc_final: 0.8271 (mt0) REVERT: G 47 LYS cc_start: 0.8953 (tptt) cc_final: 0.8688 (tptp) REVERT: J 18 GLU cc_start: 0.8188 (pp20) cc_final: 0.7589 (pp20) REVERT: J 47 LYS cc_start: 0.8017 (tttp) cc_final: 0.7608 (tttt) REVERT: K 33 GLN cc_start: 0.8483 (tt0) cc_final: 0.8187 (mt0) REVERT: L 52 GLN cc_start: 0.8272 (tt0) cc_final: 0.7990 (tt0) REVERT: L 66 ARG cc_start: 0.8299 (ptt90) cc_final: 0.8075 (ptt90) REVERT: M 9 ASP cc_start: 0.8189 (m-30) cc_final: 0.7941 (m-30) outliers start: 26 outliers final: 22 residues processed: 268 average time/residue: 0.6596 time to fit residues: 237.1121 Evaluate side-chains 260 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 238 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11761 Z= 0.158 Angle : 0.513 6.695 16127 Z= 0.261 Chirality : 0.044 0.163 1845 Planarity : 0.005 0.074 1926 Dihedral : 10.441 73.629 1939 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.58 % Rotamer: Outliers : 1.67 % Allowed : 14.01 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1289 helix: 0.44 (0.34), residues: 263 sheet: -1.31 (0.23), residues: 457 loop : 0.43 (0.30), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.004 0.001 HIS L 57 PHE 0.007 0.001 PHE B 125 TYR 0.009 0.001 TYR B 221 ARG 0.005 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 258 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8157 (t80) cc_final: 0.7894 (t80) REVERT: A 135 LYS cc_start: 0.8678 (ttmm) cc_final: 0.7504 (tptp) REVERT: A 139 LYS cc_start: 0.8867 (mttt) cc_final: 0.8646 (mttm) REVERT: E 18 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7182 (tm-30) REVERT: E 35 GLN cc_start: 0.7785 (mp10) cc_final: 0.7125 (mp10) REVERT: F 38 SER cc_start: 0.8617 (m) cc_final: 0.8067 (p) REVERT: G 35 GLN cc_start: 0.8558 (mt0) cc_final: 0.8245 (mt0) REVERT: I 55 TYR cc_start: 0.8853 (m-80) cc_final: 0.8618 (m-80) REVERT: J 18 GLU cc_start: 0.8121 (pp20) cc_final: 0.7419 (pp20) REVERT: J 47 LYS cc_start: 0.8058 (tttp) cc_final: 0.7642 (tttt) REVERT: K 33 GLN cc_start: 0.8474 (tt0) cc_final: 0.8168 (mt0) REVERT: K 37 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7871 (mt-10) REVERT: L 52 GLN cc_start: 0.8159 (tt0) cc_final: 0.7882 (tt0) REVERT: L 66 ARG cc_start: 0.8277 (ptt90) cc_final: 0.8075 (ptt90) REVERT: M 9 ASP cc_start: 0.8152 (m-30) cc_final: 0.7924 (m-30) outliers start: 20 outliers final: 18 residues processed: 272 average time/residue: 0.6640 time to fit residues: 242.2233 Evaluate side-chains 262 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 244 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 9 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN I 48 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11761 Z= 0.183 Angle : 0.521 6.366 16127 Z= 0.264 Chirality : 0.045 0.164 1845 Planarity : 0.005 0.071 1926 Dihedral : 10.374 73.599 1939 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.50 % Favored : 95.35 % Rotamer: Outliers : 1.92 % Allowed : 14.68 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1289 helix: 0.57 (0.34), residues: 268 sheet: -1.26 (0.23), residues: 457 loop : 0.54 (0.30), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 217 HIS 0.004 0.001 HIS L 57 PHE 0.007 0.001 PHE F 39 TYR 0.010 0.001 TYR K 55 ARG 0.011 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8175 (t80) cc_final: 0.7925 (t80) REVERT: A 139 LYS cc_start: 0.8856 (mttt) cc_final: 0.8604 (mttm) REVERT: E 35 GLN cc_start: 0.7779 (mp10) cc_final: 0.7275 (mp10) REVERT: G 35 GLN cc_start: 0.8549 (mt0) cc_final: 0.8244 (mt0) REVERT: I 55 TYR cc_start: 0.8850 (m-80) cc_final: 0.8622 (m-80) REVERT: J 18 GLU cc_start: 0.8157 (pp20) cc_final: 0.7421 (pp20) REVERT: K 33 GLN cc_start: 0.8501 (tt0) cc_final: 0.8178 (mt0) REVERT: K 37 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7910 (mt-10) REVERT: M 9 ASP cc_start: 0.8218 (m-30) cc_final: 0.7995 (m-30) outliers start: 23 outliers final: 22 residues processed: 270 average time/residue: 0.6615 time to fit residues: 240.6508 Evaluate side-chains 263 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 9 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11761 Z= 0.262 Angle : 0.541 6.104 16127 Z= 0.277 Chirality : 0.046 0.172 1845 Planarity : 0.005 0.074 1926 Dihedral : 10.441 73.622 1939 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.65 % Favored : 95.19 % Rotamer: Outliers : 2.67 % Allowed : 14.43 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1289 helix: 0.66 (0.34), residues: 268 sheet: -1.24 (0.23), residues: 459 loop : 0.56 (0.30), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 217 HIS 0.004 0.001 HIS E 57 PHE 0.009 0.001 PHE F 39 TYR 0.015 0.001 TYR K 55 ARG 0.007 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8186 (t80) cc_final: 0.7941 (t80) REVERT: A 139 LYS cc_start: 0.8880 (mttt) cc_final: 0.8625 (mttm) REVERT: E 18 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7510 (tm-30) REVERT: E 35 GLN cc_start: 0.7823 (mp10) cc_final: 0.7198 (mp10) REVERT: G 35 GLN cc_start: 0.8586 (mt0) cc_final: 0.8264 (mt0) REVERT: I 55 TYR cc_start: 0.8861 (m-80) cc_final: 0.8614 (m-80) REVERT: J 18 GLU cc_start: 0.8065 (pp20) cc_final: 0.7460 (pp20) REVERT: J 47 LYS cc_start: 0.7906 (tttp) cc_final: 0.7523 (tttt) REVERT: K 37 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8046 (mt-10) REVERT: N 18 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7684 (mt-10) outliers start: 32 outliers final: 31 residues processed: 266 average time/residue: 0.6632 time to fit residues: 237.6618 Evaluate side-chains 271 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 240 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 23 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 9 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN M 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11761 Z= 0.280 Angle : 0.557 6.549 16127 Z= 0.286 Chirality : 0.046 0.181 1845 Planarity : 0.005 0.073 1926 Dihedral : 10.513 73.694 1939 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.20 % Favored : 94.65 % Rotamer: Outliers : 3.09 % Allowed : 14.43 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1289 helix: 0.60 (0.34), residues: 275 sheet: -1.28 (0.23), residues: 467 loop : 0.36 (0.30), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 217 HIS 0.005 0.001 HIS E 57 PHE 0.008 0.001 PHE B 125 TYR 0.019 0.001 TYR K 55 ARG 0.007 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8236 (t80) cc_final: 0.7992 (t80) REVERT: A 139 LYS cc_start: 0.8875 (mttt) cc_final: 0.8618 (mttm) REVERT: E 35 GLN cc_start: 0.7776 (mp10) cc_final: 0.7221 (mp10) REVERT: G 35 GLN cc_start: 0.8568 (mt0) cc_final: 0.8273 (mt0) REVERT: I 55 TYR cc_start: 0.8850 (m-80) cc_final: 0.8648 (m-80) REVERT: J 18 GLU cc_start: 0.8083 (pp20) cc_final: 0.7500 (pp20) REVERT: J 31 LYS cc_start: 0.8331 (ptmt) cc_final: 0.7944 (ptmt) REVERT: J 47 LYS cc_start: 0.8049 (tttp) cc_final: 0.7631 (tttt) REVERT: M 28 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8938 (p0) REVERT: N 18 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7689 (mt-10) outliers start: 37 outliers final: 35 residues processed: 261 average time/residue: 0.6398 time to fit residues: 224.7469 Evaluate side-chains 271 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 235 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 28 ASN Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 23 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 119 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 9 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11761 Z= 0.147 Angle : 0.524 6.904 16127 Z= 0.265 Chirality : 0.044 0.166 1845 Planarity : 0.005 0.073 1926 Dihedral : 10.332 73.573 1939 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.66 % Rotamer: Outliers : 1.92 % Allowed : 16.10 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1289 helix: 0.76 (0.34), residues: 275 sheet: -1.33 (0.23), residues: 469 loop : 0.53 (0.30), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 217 HIS 0.003 0.001 HIS L 57 PHE 0.007 0.001 PHE A 123 TYR 0.008 0.001 TYR B 221 ARG 0.006 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8215 (t80) cc_final: 0.7979 (t80) REVERT: A 139 LYS cc_start: 0.8881 (mttt) cc_final: 0.8640 (mttm) REVERT: D 51 SER cc_start: 0.8128 (m) cc_final: 0.7652 (p) REVERT: E 18 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7472 (tm-30) REVERT: E 35 GLN cc_start: 0.7736 (mp10) cc_final: 0.7178 (mp10) REVERT: G 35 GLN cc_start: 0.8506 (mt0) cc_final: 0.8219 (mt0) REVERT: G 66 ARG cc_start: 0.8258 (ptm-80) cc_final: 0.8003 (ptm-80) REVERT: I 55 TYR cc_start: 0.8826 (m-80) cc_final: 0.8597 (m-80) REVERT: J 18 GLU cc_start: 0.8089 (pp20) cc_final: 0.7280 (pp20) REVERT: J 47 LYS cc_start: 0.8052 (tttp) cc_final: 0.7634 (tttt) REVERT: N 18 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7737 (mt-10) outliers start: 23 outliers final: 22 residues processed: 265 average time/residue: 0.6714 time to fit residues: 240.1585 Evaluate side-chains 263 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 184 ASN B 9 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11761 Z= 0.168 Angle : 0.516 6.555 16127 Z= 0.261 Chirality : 0.044 0.165 1845 Planarity : 0.005 0.073 1926 Dihedral : 10.222 73.581 1939 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Rotamer: Outliers : 1.50 % Allowed : 16.85 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1289 helix: 0.80 (0.34), residues: 280 sheet: -1.29 (0.23), residues: 469 loop : 0.67 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.004 0.001 HIS M 57 PHE 0.008 0.001 PHE A 123 TYR 0.009 0.001 TYR K 55 ARG 0.006 0.000 ARG L 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 247 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8213 (t80) cc_final: 0.7980 (t80) REVERT: A 139 LYS cc_start: 0.8870 (mttt) cc_final: 0.8632 (mttm) REVERT: B 116 ASP cc_start: 0.8205 (m-30) cc_final: 0.7829 (t0) REVERT: E 18 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7341 (tm-30) REVERT: E 31 LYS cc_start: 0.8164 (ptmt) cc_final: 0.7888 (ptmm) REVERT: E 35 GLN cc_start: 0.7730 (mp10) cc_final: 0.7180 (mp10) REVERT: G 35 GLN cc_start: 0.8467 (mt0) cc_final: 0.8170 (mt0) REVERT: G 66 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.8021 (ptm-80) REVERT: I 55 TYR cc_start: 0.8848 (m-80) cc_final: 0.8604 (m-80) REVERT: J 18 GLU cc_start: 0.8093 (pp20) cc_final: 0.7285 (pp20) REVERT: J 31 LYS cc_start: 0.8301 (ptmt) cc_final: 0.7953 (ptmt) REVERT: J 47 LYS cc_start: 0.8049 (tttp) cc_final: 0.7632 (tttt) REVERT: L 52 GLN cc_start: 0.8068 (tt0) cc_final: 0.7740 (tt0) REVERT: N 18 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7702 (mt-10) outliers start: 18 outliers final: 17 residues processed: 260 average time/residue: 0.6700 time to fit residues: 232.7910 Evaluate side-chains 257 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain N residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 184 ASN B 9 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN I 48 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093690 restraints weight = 45804.051| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.29 r_work: 0.2953 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11761 Z= 0.392 Angle : 0.614 6.163 16127 Z= 0.318 Chirality : 0.049 0.195 1845 Planarity : 0.005 0.076 1926 Dihedral : 10.669 73.598 1939 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.51 % Favored : 94.34 % Rotamer: Outliers : 2.42 % Allowed : 16.51 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1289 helix: 0.51 (0.34), residues: 268 sheet: -1.18 (0.23), residues: 462 loop : 0.43 (0.30), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 217 HIS 0.008 0.002 HIS M 57 PHE 0.014 0.002 PHE B 125 TYR 0.024 0.002 TYR K 55 ARG 0.006 0.001 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6327.92 seconds wall clock time: 112 minutes 13.85 seconds (6733.85 seconds total)