Starting phenix.real_space_refine (version: dev) on Mon Dec 12 00:15:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/12_2022/6i1y_0327_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/12_2022/6i1y_0327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/12_2022/6i1y_0327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/12_2022/6i1y_0327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/12_2022/6i1y_0327_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/12_2022/6i1y_0327_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.013 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 604": "NH1" <-> "NH2" Residue "F TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 604": "NH1" <-> "NH2" Residue "G TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 604": "NH1" <-> "NH2" Residue "H TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 604": "NH1" <-> "NH2" Residue "I TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 604": "NH1" <-> "NH2" Residue "J TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 604": "NH1" <-> "NH2" Residue "K TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 604": "NH1" <-> "NH2" Residue "L TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 604": "NH1" <-> "NH2" Residue "M TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 604": "NH1" <-> "NH2" Residue "N TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 604": "NH1" <-> "NH2" Residue "O TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 604": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 56520 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "B" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "C" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "D" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "E" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "F" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "G" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "H" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "I" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "J" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "K" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "L" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "M" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "N" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "O" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Time building chain proxies: 22.13, per 1000 atoms: 0.39 Number of scatterers: 56520 At special positions: 0 Unit cell: (176.66, 177.87, 192.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 11040 8.00 N 9960 7.00 C 35325 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: 17.25 Conformation dependent library (CDL) restraints added in 6.5 seconds 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13770 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 0 sheets defined 34.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 125 removed outlier: 3.830A pdb=" N ALA A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.738A pdb=" N LEU A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.547A pdb=" N ILE A 558 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 588 through 613 removed outlier: 3.603A pdb=" N ALA A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.975A pdb=" N ILE A 623 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 125 removed outlier: 3.833A pdb=" N ALA B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 5.035A pdb=" N ASP B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE B 558 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 588 through 613 removed outlier: 3.605A pdb=" N ALA B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.973A pdb=" N ILE B 623 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 649 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 311 Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.549A pdb=" N ILE C 558 " --> pdb=" O LEU C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 565 Processing helix chain 'C' and resid 588 through 613 removed outlier: 3.608A pdb=" N ALA C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.979A pdb=" N ILE C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 649 Processing helix chain 'D' and resid 110 through 113 Processing helix chain 'D' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.739A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 311 Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 554 through 558 removed outlier: 3.548A pdb=" N ILE D 558 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 565 Processing helix chain 'D' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA D 592 " --> pdb=" O ASP D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 3.976A pdb=" N ILE D 623 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 649 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 125 removed outlier: 3.833A pdb=" N ALA E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 160 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 267 removed outlier: 5.035A pdb=" N ASP E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 257 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL E 261 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 311 Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'E' and resid 397 through 404 Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 554 through 558 removed outlier: 3.549A pdb=" N ILE E 558 " --> pdb=" O LEU E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 565 Processing helix chain 'E' and resid 588 through 613 removed outlier: 3.604A pdb=" N ALA E 592 " --> pdb=" O ASP E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 623 removed outlier: 3.974A pdb=" N ILE E 623 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 649 Processing helix chain 'F' and resid 110 through 113 Processing helix chain 'F' and resid 114 through 125 removed outlier: 3.833A pdb=" N ALA F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 217 through 231 removed outlier: 3.742A pdb=" N LEU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 267 removed outlier: 5.036A pdb=" N ASP F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 257 " --> pdb=" O ASP F 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 311 Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'F' and resid 397 through 404 Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE F 558 " --> pdb=" O LEU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 565 Processing helix chain 'F' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA F 592 " --> pdb=" O ASP F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 623 removed outlier: 3.979A pdb=" N ILE F 623 " --> pdb=" O ASP F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 649 Processing helix chain 'G' and resid 110 through 113 Processing helix chain 'G' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 175 through 185 Processing helix chain 'G' and resid 217 through 231 removed outlier: 3.742A pdb=" N LEU G 231 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 267 removed outlier: 5.032A pdb=" N ASP G 256 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 257 " --> pdb=" O ASP G 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL G 261 " --> pdb=" O VAL G 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 311 Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'G' and resid 397 through 404 Processing helix chain 'G' and resid 405 through 407 No H-bonds generated for 'chain 'G' and resid 405 through 407' Processing helix chain 'G' and resid 554 through 558 removed outlier: 3.551A pdb=" N ILE G 558 " --> pdb=" O LEU G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 561 through 565 Processing helix chain 'G' and resid 588 through 613 removed outlier: 3.608A pdb=" N ALA G 592 " --> pdb=" O ASP G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 623 removed outlier: 3.978A pdb=" N ILE G 623 " --> pdb=" O ASP G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 649 Processing helix chain 'H' and resid 110 through 113 Processing helix chain 'H' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 217 through 231 removed outlier: 3.740A pdb=" N LEU H 231 " --> pdb=" O LEU H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL H 257 " --> pdb=" O ASP H 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL H 261 " --> pdb=" O VAL H 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 311 Processing helix chain 'H' and resid 358 through 369 Processing helix chain 'H' and resid 397 through 404 Processing helix chain 'H' and resid 405 through 407 No H-bonds generated for 'chain 'H' and resid 405 through 407' Processing helix chain 'H' and resid 554 through 558 removed outlier: 3.548A pdb=" N ILE H 558 " --> pdb=" O LEU H 555 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 565 Processing helix chain 'H' and resid 588 through 613 removed outlier: 3.605A pdb=" N ALA H 592 " --> pdb=" O ASP H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 623 removed outlier: 3.976A pdb=" N ILE H 623 " --> pdb=" O ASP H 620 " (cutoff:3.500A) Processing helix chain 'H' and resid 636 through 649 Processing helix chain 'I' and resid 110 through 113 Processing helix chain 'I' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 161 through 163 No H-bonds generated for 'chain 'I' and resid 161 through 163' Processing helix chain 'I' and resid 175 through 185 Processing helix chain 'I' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU I 231 " --> pdb=" O LEU I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP I 256 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL I 257 " --> pdb=" O ASP I 253 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL I 261 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 311 Processing helix chain 'I' and resid 358 through 369 Processing helix chain 'I' and resid 397 through 404 Processing helix chain 'I' and resid 405 through 407 No H-bonds generated for 'chain 'I' and resid 405 through 407' Processing helix chain 'I' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE I 558 " --> pdb=" O LEU I 555 " (cutoff:3.500A) Processing helix chain 'I' and resid 561 through 565 Processing helix chain 'I' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA I 592 " --> pdb=" O ASP I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 623 removed outlier: 3.974A pdb=" N ILE I 623 " --> pdb=" O ASP I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 636 through 649 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 160 Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 175 through 185 Processing helix chain 'J' and resid 217 through 231 removed outlier: 3.740A pdb=" N LEU J 231 " --> pdb=" O LEU J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL J 257 " --> pdb=" O ASP J 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL J 261 " --> pdb=" O VAL J 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 311 Processing helix chain 'J' and resid 358 through 369 Processing helix chain 'J' and resid 397 through 404 Processing helix chain 'J' and resid 405 through 407 No H-bonds generated for 'chain 'J' and resid 405 through 407' Processing helix chain 'J' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE J 558 " --> pdb=" O LEU J 555 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 565 Processing helix chain 'J' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA J 592 " --> pdb=" O ASP J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 623 removed outlier: 3.979A pdb=" N ILE J 623 " --> pdb=" O ASP J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 649 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 160 Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 175 through 185 Processing helix chain 'K' and resid 217 through 231 removed outlier: 3.739A pdb=" N LEU K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP K 256 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL K 257 " --> pdb=" O ASP K 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL K 261 " --> pdb=" O VAL K 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 311 Processing helix chain 'K' and resid 358 through 369 Processing helix chain 'K' and resid 397 through 404 Processing helix chain 'K' and resid 405 through 407 No H-bonds generated for 'chain 'K' and resid 405 through 407' Processing helix chain 'K' and resid 554 through 558 removed outlier: 3.548A pdb=" N ILE K 558 " --> pdb=" O LEU K 555 " (cutoff:3.500A) Processing helix chain 'K' and resid 561 through 565 Processing helix chain 'K' and resid 588 through 613 removed outlier: 3.608A pdb=" N ALA K 592 " --> pdb=" O ASP K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 623 removed outlier: 3.981A pdb=" N ILE K 623 " --> pdb=" O ASP K 620 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 649 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA L 125 " --> pdb=" O LEU L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 160 Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'L' and resid 175 through 185 Processing helix chain 'L' and resid 217 through 231 removed outlier: 3.740A pdb=" N LEU L 231 " --> pdb=" O LEU L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 267 removed outlier: 5.030A pdb=" N ASP L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL L 257 " --> pdb=" O ASP L 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL L 261 " --> pdb=" O VAL L 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 311 Processing helix chain 'L' and resid 358 through 369 Processing helix chain 'L' and resid 397 through 404 Processing helix chain 'L' and resid 405 through 407 No H-bonds generated for 'chain 'L' and resid 405 through 407' Processing helix chain 'L' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE L 558 " --> pdb=" O LEU L 555 " (cutoff:3.500A) Processing helix chain 'L' and resid 561 through 565 Processing helix chain 'L' and resid 588 through 613 removed outlier: 3.605A pdb=" N ALA L 592 " --> pdb=" O ASP L 588 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 623 removed outlier: 3.974A pdb=" N ILE L 623 " --> pdb=" O ASP L 620 " (cutoff:3.500A) Processing helix chain 'L' and resid 636 through 649 Processing helix chain 'M' and resid 110 through 113 Processing helix chain 'M' and resid 114 through 125 removed outlier: 3.833A pdb=" N ALA M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 160 Processing helix chain 'M' and resid 161 through 163 No H-bonds generated for 'chain 'M' and resid 161 through 163' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 217 through 231 removed outlier: 3.740A pdb=" N LEU M 231 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 267 removed outlier: 5.036A pdb=" N ASP M 256 " --> pdb=" O GLU M 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL M 257 " --> pdb=" O ASP M 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL M 261 " --> pdb=" O VAL M 257 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN M 264 " --> pdb=" O GLY M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 299 through 311 Processing helix chain 'M' and resid 358 through 369 Processing helix chain 'M' and resid 397 through 404 Processing helix chain 'M' and resid 405 through 407 No H-bonds generated for 'chain 'M' and resid 405 through 407' Processing helix chain 'M' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE M 558 " --> pdb=" O LEU M 555 " (cutoff:3.500A) Processing helix chain 'M' and resid 561 through 565 Processing helix chain 'M' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA M 592 " --> pdb=" O ASP M 588 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 623 removed outlier: 3.975A pdb=" N ILE M 623 " --> pdb=" O ASP M 620 " (cutoff:3.500A) Processing helix chain 'M' and resid 636 through 649 Processing helix chain 'N' and resid 110 through 113 Processing helix chain 'N' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA N 125 " --> pdb=" O LEU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 160 Processing helix chain 'N' and resid 161 through 163 No H-bonds generated for 'chain 'N' and resid 161 through 163' Processing helix chain 'N' and resid 175 through 185 Processing helix chain 'N' and resid 217 through 231 removed outlier: 3.742A pdb=" N LEU N 231 " --> pdb=" O LEU N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 267 removed outlier: 5.035A pdb=" N ASP N 256 " --> pdb=" O GLU N 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL N 257 " --> pdb=" O ASP N 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL N 261 " --> pdb=" O VAL N 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN N 264 " --> pdb=" O GLY N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 311 Processing helix chain 'N' and resid 358 through 369 Processing helix chain 'N' and resid 397 through 404 Processing helix chain 'N' and resid 405 through 407 No H-bonds generated for 'chain 'N' and resid 405 through 407' Processing helix chain 'N' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE N 558 " --> pdb=" O LEU N 555 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 565 Processing helix chain 'N' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA N 592 " --> pdb=" O ASP N 588 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 623 removed outlier: 3.979A pdb=" N ILE N 623 " --> pdb=" O ASP N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 636 through 649 Processing helix chain 'O' and resid 110 through 113 Processing helix chain 'O' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA O 125 " --> pdb=" O LEU O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 160 Processing helix chain 'O' and resid 161 through 163 No H-bonds generated for 'chain 'O' and resid 161 through 163' Processing helix chain 'O' and resid 175 through 185 Processing helix chain 'O' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU O 231 " --> pdb=" O LEU O 227 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 267 removed outlier: 5.032A pdb=" N ASP O 256 " --> pdb=" O GLU O 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL O 257 " --> pdb=" O ASP O 253 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL O 261 " --> pdb=" O VAL O 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN O 264 " --> pdb=" O GLY O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 311 Processing helix chain 'O' and resid 358 through 369 Processing helix chain 'O' and resid 397 through 404 Processing helix chain 'O' and resid 405 through 407 No H-bonds generated for 'chain 'O' and resid 405 through 407' Processing helix chain 'O' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE O 558 " --> pdb=" O LEU O 555 " (cutoff:3.500A) Processing helix chain 'O' and resid 561 through 565 Processing helix chain 'O' and resid 588 through 613 removed outlier: 3.607A pdb=" N ALA O 592 " --> pdb=" O ASP O 588 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 623 removed outlier: 3.976A pdb=" N ILE O 623 " --> pdb=" O ASP O 620 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 649 1530 hydrogen bonds defined for protein. 4365 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: 13.50 Time building geometry restraints manager: 18.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 10390 1.30 - 1.44: 11923 1.44 - 1.57: 34312 1.57 - 1.70: 0 1.70 - 1.83: 390 Bond restraints: 57015 Sorted by residual: bond pdb=" C ASN N 524 " pdb=" O ASN N 524 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.14e-02 7.69e+03 3.36e+01 bond pdb=" C ASN E 524 " pdb=" O ASN E 524 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.14e-02 7.69e+03 3.30e+01 bond pdb=" C ASN M 524 " pdb=" O ASN M 524 " ideal model delta sigma weight residual 1.236 1.170 0.065 1.14e-02 7.69e+03 3.29e+01 bond pdb=" C ASN F 524 " pdb=" O ASN F 524 " ideal model delta sigma weight residual 1.236 1.171 0.065 1.14e-02 7.69e+03 3.28e+01 bond pdb=" C ASN G 524 " pdb=" O ASN G 524 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.19e-02 7.06e+03 3.10e+01 ... (remaining 57010 not shown) Histogram of bond angle deviations from ideal: 97.14 - 104.57: 995 104.57 - 111.99: 26432 111.99 - 119.42: 27738 119.42 - 126.85: 21609 126.85 - 134.27: 401 Bond angle restraints: 77175 Sorted by residual: angle pdb=" C GLU N 503 " pdb=" N VAL N 504 " pdb=" CA VAL N 504 " ideal model delta sigma weight residual 122.91 109.11 13.80 1.43e+00 4.89e-01 9.31e+01 angle pdb=" C GLU C 503 " pdb=" N VAL C 504 " pdb=" CA VAL C 504 " ideal model delta sigma weight residual 122.91 109.13 13.78 1.43e+00 4.89e-01 9.29e+01 angle pdb=" C GLU J 503 " pdb=" N VAL J 504 " pdb=" CA VAL J 504 " ideal model delta sigma weight residual 122.91 109.17 13.74 1.43e+00 4.89e-01 9.24e+01 angle pdb=" C GLU G 503 " pdb=" N VAL G 504 " pdb=" CA VAL G 504 " ideal model delta sigma weight residual 122.91 109.18 13.73 1.43e+00 4.89e-01 9.22e+01 angle pdb=" C GLU F 503 " pdb=" N VAL F 504 " pdb=" CA VAL F 504 " ideal model delta sigma weight residual 122.91 109.21 13.70 1.43e+00 4.89e-01 9.18e+01 ... (remaining 77170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 30832 14.38 - 28.76: 3414 28.76 - 43.13: 831 43.13 - 57.51: 128 57.51 - 71.89: 60 Dihedral angle restraints: 35265 sinusoidal: 14010 harmonic: 21255 Sorted by residual: dihedral pdb=" CA ALA A 298 " pdb=" C ALA A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta harmonic sigma weight residual 180.00 139.69 40.31 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ALA E 298 " pdb=" C ALA E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta harmonic sigma weight residual 180.00 139.73 40.27 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA ALA C 298 " pdb=" C ALA C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta harmonic sigma weight residual 180.00 139.73 40.27 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 35262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4193 0.069 - 0.137: 3655 0.137 - 0.206: 1302 0.206 - 0.275: 241 0.275 - 0.343: 29 Chirality restraints: 9420 Sorted by residual: chirality pdb=" CA ASP G 531 " pdb=" N ASP G 531 " pdb=" C ASP G 531 " pdb=" CB ASP G 531 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP E 531 " pdb=" N ASP E 531 " pdb=" C ASP E 531 " pdb=" CB ASP E 531 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP L 531 " pdb=" N ASP L 531 " pdb=" C ASP L 531 " pdb=" CB ASP L 531 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 9417 not shown) Planarity restraints: 10065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 565 " -0.082 2.00e-02 2.50e+03 7.58e-02 1.01e+02 pdb=" CG PHE J 565 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE J 565 " 0.130 2.00e-02 2.50e+03 pdb=" CD2 PHE J 565 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE J 565 " -0.087 2.00e-02 2.50e+03 pdb=" CE2 PHE J 565 " 0.058 2.00e-02 2.50e+03 pdb=" CZ PHE J 565 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 565 " -0.075 2.00e-02 2.50e+03 7.51e-02 9.88e+01 pdb=" CG PHE F 565 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE F 565 " 0.128 2.00e-02 2.50e+03 pdb=" CD2 PHE F 565 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE F 565 " -0.087 2.00e-02 2.50e+03 pdb=" CE2 PHE F 565 " 0.066 2.00e-02 2.50e+03 pdb=" CZ PHE F 565 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 565 " -0.068 2.00e-02 2.50e+03 7.42e-02 9.63e+01 pdb=" CG PHE H 565 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE H 565 " 0.128 2.00e-02 2.50e+03 pdb=" CD2 PHE H 565 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE H 565 " -0.087 2.00e-02 2.50e+03 pdb=" CE2 PHE H 565 " 0.071 2.00e-02 2.50e+03 pdb=" CZ PHE H 565 " -0.049 2.00e-02 2.50e+03 ... (remaining 10062 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 150 2.02 - 2.74: 8015 2.74 - 3.46: 85586 3.46 - 4.18: 140918 4.18 - 4.90: 244311 Nonbonded interactions: 478980 Sorted by model distance: nonbonded pdb=" O GLN H 312 " pdb=" OH TYR I 245 " model vdw 1.301 2.440 nonbonded pdb=" O GLN K 312 " pdb=" OH TYR L 245 " model vdw 1.302 2.440 nonbonded pdb=" O GLN D 312 " pdb=" OH TYR E 245 " model vdw 1.304 2.440 nonbonded pdb=" OH TYR A 245 " pdb=" O GLN O 312 " model vdw 1.306 2.440 nonbonded pdb=" O GLN A 312 " pdb=" OH TYR B 245 " model vdw 1.307 2.440 ... (remaining 478975 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 35325 2.51 5 N 9960 2.21 5 O 11040 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.500 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: 0.030 Extract box with map and model: 7.240 Check model and map are aligned: 0.610 Convert atoms to be neutral: 0.380 Process input model: 101.100 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.015 0.093 57015 Z= 0.968 Angle : 2.010 13.799 77175 Z= 1.399 Chirality : 0.100 0.343 9420 Planarity : 0.023 0.123 10065 Dihedral : 13.306 71.888 21495 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 75.63 Ramachandran Plot: Outliers : 3.29 % Allowed : 10.91 % Favored : 85.80 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.84 % 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: -5.20 (0.08), residues: 7290 helix: -3.58 (0.08), residues: 2070 sheet: -3.21 (0.08), residues: 2895 loop : -3.04 (0.09), residues: 2325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1376 time to evaluate : 4.872 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 outliers start: 45 outliers final: 18 residues processed: 1391 average time/residue: 0.5416 time to fit residues: 1236.2118 Evaluate side-chains 819 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 801 time to evaluate : 4.908 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4476 time to fit residues: 20.9630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 1.9990 chunk 557 optimal weight: 0.9980 chunk 309 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 375 optimal weight: 0.5980 chunk 297 optimal weight: 8.9990 chunk 576 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 350 optimal weight: 2.9990 chunk 428 optimal weight: 0.7980 chunk 667 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS D 241 ASN ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 241 ASN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN E 408 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS F 241 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 241 ASN ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 HIS G 307 GLN ** G 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 ASN H 289 GLN ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN H 635 HIS I 132 HIS I 241 ASN ** I 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS J 241 ASN ** J 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 408 ASN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 524 ASN J 635 HIS K 241 ASN ** K 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 GLN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 HIS ** L 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 635 HIS M 132 HIS M 241 ASN ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 ASN ** M 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 635 HIS N 241 ASN ** N 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 GLN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 241 ASN ** O 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN O 635 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 57015 Z= 0.276 Angle : 0.737 8.769 77175 Z= 0.380 Chirality : 0.049 0.214 9420 Planarity : 0.006 0.104 10065 Dihedral : 5.938 22.509 7875 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.95 % Favored : 93.84 % Rotamer Outliers : 2.45 % 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: -3.35 (0.09), residues: 7290 helix: -1.35 (0.10), residues: 2280 sheet: -2.57 (0.09), residues: 2580 loop : -2.28 (0.11), residues: 2430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1089 time to evaluate : 4.973 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 outliers start: 152 outliers final: 36 residues processed: 1171 average time/residue: 0.4946 time to fit residues: 996.0986 Evaluate side-chains 876 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 840 time to evaluate : 4.885 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4154 time to fit residues: 34.3515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 555 optimal weight: 3.9990 chunk 454 optimal weight: 5.9990 chunk 184 optimal weight: 0.4980 chunk 668 optimal weight: 0.0030 chunk 722 optimal weight: 4.9990 chunk 595 optimal weight: 20.0000 chunk 663 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 536 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 288 HIS B 312 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN C 264 ASN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 ASN C 502 GLN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 312 GLN D 408 ASN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 264 ASN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 GLN E 533 GLN F 264 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 HIS ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 502 GLN F 522 GLN F 533 GLN G 264 ASN ** G 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 ASN G 502 GLN G 533 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 408 ASN H 502 GLN I 264 ASN I 288 HIS I 307 GLN ** I 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 ASN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 264 ASN J 289 GLN ** J 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 502 GLN ** K 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 HIS ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 408 ASN K 502 GLN ** L 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 HIS ** L 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 264 ASN ** M 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 502 GLN M 524 ASN N 264 ASN ** N 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 408 ASN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 264 ASN O 288 HIS ** O 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 502 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 57015 Z= 0.205 Angle : 0.617 7.412 77175 Z= 0.312 Chirality : 0.047 0.212 9420 Planarity : 0.005 0.101 10065 Dihedral : 4.955 19.355 7875 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.51 % Favored : 95.28 % Rotamer Outliers : 2.33 % 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: -2.60 (0.09), residues: 7290 helix: -0.51 (0.10), residues: 2370 sheet: -2.28 (0.09), residues: 2715 loop : -1.91 (0.12), residues: 2205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 902 time to evaluate : 6.193 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 51 residues processed: 1010 average time/residue: 0.4951 time to fit residues: 860.6164 Evaluate side-chains 790 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 739 time to evaluate : 5.998 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.3940 time to fit residues: 44.6012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 0.0020 chunk 502 optimal weight: 20.0000 chunk 347 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 319 optimal weight: 6.9990 chunk 449 optimal weight: 9.9990 chunk 671 optimal weight: 3.9990 chunk 710 optimal weight: 0.4980 chunk 350 optimal weight: 9.9990 chunk 636 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 overall best weight: 3.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 288 HIS D 312 GLN D 502 GLN E 288 HIS E 408 ASN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN F 533 GLN G 408 ASN H 288 HIS ** H 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 HIS J 533 GLN K 264 ASN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 ASN L 319 GLN L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 288 HIS M 307 GLN N 288 HIS N 312 GLN ** N 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 57015 Z= 0.415 Angle : 0.680 8.489 77175 Z= 0.343 Chirality : 0.047 0.214 9420 Planarity : 0.006 0.097 10065 Dihedral : 5.059 20.487 7875 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.11 % Favored : 91.69 % Rotamer Outliers : 3.86 % 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: -2.30 (0.09), residues: 7290 helix: -0.20 (0.11), residues: 2355 sheet: -2.11 (0.09), residues: 2700 loop : -1.82 (0.12), residues: 2235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 751 time to evaluate : 4.916 Fit side-chains revert: symmetry clash outliers start: 240 outliers final: 105 residues processed: 945 average time/residue: 0.4944 time to fit residues: 804.3995 Evaluate side-chains 767 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 662 time to evaluate : 4.922 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 0.3935 time to fit residues: 84.9664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 6.9990 chunk 403 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 528 optimal weight: 0.7980 chunk 293 optimal weight: 6.9990 chunk 606 optimal weight: 1.9990 chunk 491 optimal weight: 0.0980 chunk 0 optimal weight: 30.0000 chunk 362 optimal weight: 4.9990 chunk 637 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN B 241 ASN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN E 312 GLN E 524 ASN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN G 266 GLN G 489 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 GLN L 408 ASN L 502 GLN M 522 GLN ** N 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 502 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 57015 Z= 0.232 Angle : 0.586 8.622 77175 Z= 0.296 Chirality : 0.046 0.202 9420 Planarity : 0.005 0.094 10065 Dihedral : 4.678 20.059 7875 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.90 % Favored : 94.90 % Rotamer Outliers : 2.22 % 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: -1.97 (0.10), residues: 7290 helix: 0.18 (0.11), residues: 2310 sheet: -2.02 (0.09), residues: 2685 loop : -1.61 (0.12), residues: 2295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 755 time to evaluate : 4.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 56 residues processed: 862 average time/residue: 0.5021 time to fit residues: 742.9726 Evaluate side-chains 709 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 653 time to evaluate : 4.842 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4000 time to fit residues: 48.7130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 7.9990 chunk 639 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 417 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 711 optimal weight: 4.9990 chunk 590 optimal weight: 8.9990 chunk 329 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 373 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 ASN G 266 GLN G 576 ASN H 601 ASN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN N 240 ASN ** N 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 489 GLN N 601 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.086 57015 Z= 0.536 Angle : 0.738 8.225 77175 Z= 0.375 Chirality : 0.049 0.222 9420 Planarity : 0.006 0.092 10065 Dihedral : 5.202 21.513 7875 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.93 % Favored : 90.86 % Rotamer Outliers : 3.03 % 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: -2.33 (0.09), residues: 7290 helix: -0.06 (0.11), residues: 2325 sheet: -2.22 (0.09), residues: 2730 loop : -1.87 (0.12), residues: 2235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 690 time to evaluate : 5.025 Fit side-chains revert: symmetry clash outliers start: 188 outliers final: 90 residues processed: 836 average time/residue: 0.4958 time to fit residues: 717.8718 Evaluate side-chains 730 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 640 time to evaluate : 4.969 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 0.3970 time to fit residues: 74.8452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 405 optimal weight: 0.9980 chunk 519 optimal weight: 4.9990 chunk 402 optimal weight: 6.9990 chunk 598 optimal weight: 0.9990 chunk 397 optimal weight: 7.9990 chunk 708 optimal weight: 2.9990 chunk 443 optimal weight: 6.9990 chunk 431 optimal weight: 1.9990 chunk 327 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 266 GLN B 312 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN H 489 GLN ** I 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 576 ASN N 506 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 57015 Z= 0.248 Angle : 0.606 9.225 77175 Z= 0.309 Chirality : 0.046 0.256 9420 Planarity : 0.005 0.090 10065 Dihedral : 4.747 21.440 7875 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.12 % Favored : 94.68 % Rotamer Outliers : 1.08 % 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: -1.99 (0.10), residues: 7290 helix: 0.21 (0.11), residues: 2310 sheet: -2.18 (0.09), residues: 2700 loop : -1.46 (0.13), residues: 2280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 720 time to evaluate : 4.923 Fit side-chains outliers start: 67 outliers final: 23 residues processed: 765 average time/residue: 0.5079 time to fit residues: 664.5184 Evaluate side-chains 678 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 655 time to evaluate : 4.917 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4186 time to fit residues: 24.5871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 0.8980 chunk 282 optimal weight: 0.9980 chunk 423 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 450 optimal weight: 5.9990 chunk 482 optimal weight: 7.9990 chunk 350 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 556 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN C 266 GLN C 522 GLN ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 ASN H 489 GLN ** I 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN M 506 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 57015 Z= 0.231 Angle : 0.594 13.074 77175 Z= 0.300 Chirality : 0.046 0.202 9420 Planarity : 0.005 0.087 10065 Dihedral : 4.537 19.877 7875 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.28 % Favored : 92.51 % Rotamer Outliers : 0.87 % 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: -1.92 (0.10), residues: 7290 helix: 0.33 (0.11), residues: 2325 sheet: -2.18 (0.09), residues: 2760 loop : -1.41 (0.13), residues: 2205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 678 time to evaluate : 4.937 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 23 residues processed: 715 average time/residue: 0.5279 time to fit residues: 645.1142 Evaluate side-chains 653 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 630 time to evaluate : 4.915 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3990 time to fit residues: 24.3002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 3.9990 chunk 678 optimal weight: 8.9990 chunk 619 optimal weight: 0.9980 chunk 660 optimal weight: 2.9990 chunk 397 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 518 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 596 optimal weight: 7.9990 chunk 624 optimal weight: 0.9980 chunk 657 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN G 522 GLN ** I 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 57015 Z= 0.243 Angle : 0.601 11.493 77175 Z= 0.303 Chirality : 0.046 0.252 9420 Planarity : 0.005 0.086 10065 Dihedral : 4.523 20.311 7875 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.55 % Rotamer Outliers : 0.74 % 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: -1.77 (0.10), residues: 7290 helix: 0.44 (0.11), residues: 2310 sheet: -2.18 (0.09), residues: 2790 loop : -1.13 (0.13), residues: 2190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 646 time to evaluate : 5.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 28 residues processed: 672 average time/residue: 0.5188 time to fit residues: 597.8938 Evaluate side-chains 655 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 627 time to evaluate : 4.994 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3996 time to fit residues: 28.0791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 7.9990 chunk 698 optimal weight: 3.9990 chunk 426 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 485 optimal weight: 0.2980 chunk 732 optimal weight: 9.9990 chunk 673 optimal weight: 3.9990 chunk 583 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 450 optimal weight: 7.9990 chunk 357 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 GLN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 57015 Z= 0.322 Angle : 0.643 13.883 77175 Z= 0.324 Chirality : 0.046 0.205 9420 Planarity : 0.006 0.084 10065 Dihedral : 4.696 21.340 7875 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.18 % Favored : 91.62 % Rotamer Outliers : 0.24 % 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: -1.83 (0.10), residues: 7290 helix: 0.42 (0.11), residues: 2310 sheet: -2.25 (0.09), residues: 2790 loop : -1.15 (0.13), residues: 2190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 648 time to evaluate : 4.977 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 658 average time/residue: 0.5176 time to fit residues: 581.9650 Evaluate side-chains 637 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 628 time to evaluate : 4.894 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4020 time to fit residues: 13.5430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 4.9990 chunk 621 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 537 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 162 optimal weight: 5.9990 chunk 584 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 599 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 0.0770 overall best weight: 1.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.193877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155421 restraints weight = 72398.030| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.86 r_work: 0.3721 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 57015 Z= 0.220 Angle : 0.600 10.621 77175 Z= 0.303 Chirality : 0.046 0.287 9420 Planarity : 0.005 0.083 10065 Dihedral : 4.496 20.769 7875 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.92 % Rotamer Outliers : 0.26 % 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: -1.67 (0.10), residues: 7290 helix: 0.55 (0.11), residues: 2310 sheet: -2.19 (0.09), residues: 2820 loop : -0.96 (0.14), residues: 2160 =============================================================================== Job complete usr+sys time: 13076.15 seconds wall clock time: 230 minutes 26.28 seconds (13826.28 seconds total)