Starting phenix.real_space_refine on Mon Mar 11 08:27:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/03_2024/6i1y_0327_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/03_2024/6i1y_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_0327/03_2024/6i1y_0327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/03_2024/6i1y_0327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/03_2024/6i1y_0327_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/03_2024/6i1y_0327_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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. 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-5265/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: 20.62, per 1000 atoms: 0.36 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: 16.53 Conformation dependent library (CDL) restraints added in 8.1 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: 3.07 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: 12.71 Time building geometry restraints manager: 18.40 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 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: 0.750 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: 0.040 Extract box with map and model: 5.440 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 103.970 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 % Allowed : 5.56 % Favored : 93.72 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.019 TRP E 341 HIS 0.049 0.019 HIS A 288 PHE 0.130 0.032 PHE J 565 TYR 0.083 0.025 TYR N 600 ARG 0.080 0.006 ARG F 477 *********************** 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 : 4.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8007 (tpp) cc_final: 0.7630 (ttm) REVERT: A 412 MET cc_start: 0.8338 (mtp) cc_final: 0.8050 (ttt) REVERT: A 492 GLU cc_start: 0.8995 (tp30) cc_final: 0.8686 (tt0) REVERT: A 533 GLN cc_start: 0.8673 (mt0) cc_final: 0.8462 (tt0) REVERT: A 590 MET cc_start: 0.8239 (ttm) cc_final: 0.7989 (tmm) REVERT: A 619 ASP cc_start: 0.8885 (m-30) cc_final: 0.8637 (t70) REVERT: A 633 LYS cc_start: 0.7596 (tppt) cc_final: 0.7188 (tptt) REVERT: A 634 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.8144 (ttp-170) REVERT: A 635 HIS cc_start: 0.8460 (m90) cc_final: 0.8103 (m90) REVERT: B 252 GLU cc_start: 0.9394 (tp30) cc_final: 0.8728 (pt0) REVERT: B 303 MET cc_start: 0.7864 (tpp) cc_final: 0.7545 (ttm) REVERT: B 308 GLU cc_start: 0.8785 (tt0) cc_final: 0.8341 (tp30) REVERT: B 312 GLN cc_start: 0.8448 (mt0) cc_final: 0.8143 (mt0) REVERT: B 412 MET cc_start: 0.8312 (mtp) cc_final: 0.8064 (ttt) REVERT: B 492 GLU cc_start: 0.8915 (tp30) cc_final: 0.8595 (tt0) REVERT: B 501 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8634 (tm-30) REVERT: B 533 GLN cc_start: 0.8624 (mt0) cc_final: 0.8373 (tt0) REVERT: B 588 ASP cc_start: 0.8278 (m-30) cc_final: 0.8044 (t70) REVERT: B 590 MET cc_start: 0.8379 (ttm) cc_final: 0.8154 (tmm) REVERT: B 619 ASP cc_start: 0.8653 (m-30) cc_final: 0.8345 (t70) REVERT: B 634 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8376 (ttp-170) REVERT: C 308 GLU cc_start: 0.8799 (tt0) cc_final: 0.8521 (tp30) REVERT: C 412 MET cc_start: 0.8216 (mtp) cc_final: 0.7913 (mmp) REVERT: C 492 GLU cc_start: 0.8932 (tp30) cc_final: 0.8606 (tt0) REVERT: C 533 GLN cc_start: 0.8872 (mt0) cc_final: 0.8579 (tt0) REVERT: C 590 MET cc_start: 0.8308 (ttm) cc_final: 0.8035 (tmm) REVERT: C 619 ASP cc_start: 0.8714 (m-30) cc_final: 0.8420 (t70) REVERT: C 635 HIS cc_start: 0.8603 (m90) cc_final: 0.8362 (m90) REVERT: D 307 GLN cc_start: 0.8808 (tp40) cc_final: 0.8577 (tp-100) REVERT: D 308 GLU cc_start: 0.8896 (tt0) cc_final: 0.8393 (tp30) REVERT: D 312 GLN cc_start: 0.8601 (mt0) cc_final: 0.8167 (mt0) REVERT: D 412 MET cc_start: 0.8221 (mtp) cc_final: 0.7931 (mmp) REVERT: D 492 GLU cc_start: 0.9024 (tp30) cc_final: 0.8735 (tt0) REVERT: D 501 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8560 (tm-30) REVERT: D 522 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8808 (pt0) REVERT: D 533 GLN cc_start: 0.8636 (mt0) cc_final: 0.8395 (tt0) REVERT: D 573 GLU cc_start: 0.8840 (tt0) cc_final: 0.8583 (mt-10) REVERT: D 590 MET cc_start: 0.8499 (ttm) cc_final: 0.8272 (tmm) REVERT: D 619 ASP cc_start: 0.8601 (m-30) cc_final: 0.8358 (t0) REVERT: D 634 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8353 (ttp-170) REVERT: D 635 HIS cc_start: 0.8274 (m90) cc_final: 0.7855 (m90) REVERT: E 303 MET cc_start: 0.8169 (tpp) cc_final: 0.7892 (ttm) REVERT: E 308 GLU cc_start: 0.8746 (tt0) cc_final: 0.8444 (tp30) REVERT: E 412 MET cc_start: 0.8355 (mtp) cc_final: 0.8118 (mpp) REVERT: E 492 GLU cc_start: 0.8817 (tp30) cc_final: 0.8519 (tt0) REVERT: E 501 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8790 (mp0) REVERT: E 524 ASN cc_start: 0.8992 (p0) cc_final: 0.8701 (p0) REVERT: E 533 GLN cc_start: 0.8842 (mt0) cc_final: 0.8541 (tt0) REVERT: E 619 ASP cc_start: 0.8696 (m-30) cc_final: 0.8449 (t70) REVERT: F 303 MET cc_start: 0.8145 (tpp) cc_final: 0.7776 (ttm) REVERT: F 329 MET cc_start: 0.9061 (ttp) cc_final: 0.8850 (ttp) REVERT: F 412 MET cc_start: 0.8206 (mtp) cc_final: 0.7978 (mmp) REVERT: F 492 GLU cc_start: 0.8934 (tp30) cc_final: 0.8662 (tt0) REVERT: F 522 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8856 (pt0) REVERT: F 533 GLN cc_start: 0.8745 (mt0) cc_final: 0.8533 (tt0) REVERT: F 534 MET cc_start: 0.9197 (ttm) cc_final: 0.8941 (ttp) REVERT: F 590 MET cc_start: 0.8512 (ttm) cc_final: 0.8302 (tmm) REVERT: F 619 ASP cc_start: 0.8733 (m-30) cc_final: 0.8496 (t0) REVERT: F 634 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8274 (ttp-170) REVERT: G 412 MET cc_start: 0.8137 (mtp) cc_final: 0.7808 (mmp) REVERT: G 485 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8704 (ttmt) REVERT: G 492 GLU cc_start: 0.8998 (tp30) cc_final: 0.8692 (tt0) REVERT: G 522 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8769 (pt0) REVERT: G 533 GLN cc_start: 0.8872 (mt0) cc_final: 0.8603 (tt0) REVERT: G 619 ASP cc_start: 0.8817 (m-30) cc_final: 0.8550 (t0) REVERT: G 634 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8156 (ttp-170) REVERT: H 252 GLU cc_start: 0.9395 (tp30) cc_final: 0.9191 (tp30) REVERT: H 303 MET cc_start: 0.8124 (tpp) cc_final: 0.7765 (ttm) REVERT: H 308 GLU cc_start: 0.8657 (tt0) cc_final: 0.8119 (tp30) REVERT: H 312 GLN cc_start: 0.8571 (mt0) cc_final: 0.8182 (mt0) REVERT: H 412 MET cc_start: 0.8175 (mtp) cc_final: 0.7898 (mmt) REVERT: H 492 GLU cc_start: 0.8886 (tp30) cc_final: 0.8534 (tt0) REVERT: H 533 GLN cc_start: 0.8754 (mt0) cc_final: 0.8435 (tt0) REVERT: H 573 GLU cc_start: 0.8806 (tt0) cc_final: 0.8537 (mt-10) REVERT: H 590 MET cc_start: 0.8314 (ttm) cc_final: 0.8079 (tmm) REVERT: H 619 ASP cc_start: 0.8806 (m-30) cc_final: 0.8573 (t70) REVERT: H 634 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8258 (ttp-170) REVERT: H 635 HIS cc_start: 0.8468 (m90) cc_final: 0.8097 (m90) REVERT: I 303 MET cc_start: 0.8163 (tpp) cc_final: 0.7827 (ttm) REVERT: I 412 MET cc_start: 0.8116 (mtp) cc_final: 0.7756 (mmp) REVERT: I 492 GLU cc_start: 0.8907 (tp30) cc_final: 0.8584 (tt0) REVERT: I 533 GLN cc_start: 0.8627 (mt0) cc_final: 0.8350 (tt0) REVERT: I 618 MET cc_start: 0.8758 (mtp) cc_final: 0.8451 (mtp) REVERT: I 619 ASP cc_start: 0.8738 (m-30) cc_final: 0.8499 (t70) REVERT: I 634 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8321 (ttp-170) REVERT: J 303 MET cc_start: 0.7910 (tpp) cc_final: 0.7584 (ttm) REVERT: J 329 MET cc_start: 0.9091 (ttp) cc_final: 0.8865 (ttp) REVERT: J 412 MET cc_start: 0.8249 (mtp) cc_final: 0.8003 (mmp) REVERT: J 492 GLU cc_start: 0.8860 (tp30) cc_final: 0.8596 (tt0) REVERT: J 522 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8811 (pt0) REVERT: J 533 GLN cc_start: 0.8660 (mt0) cc_final: 0.8419 (tt0) REVERT: J 588 ASP cc_start: 0.8055 (m-30) cc_final: 0.7845 (t70) REVERT: J 619 ASP cc_start: 0.8738 (m-30) cc_final: 0.8462 (t0) REVERT: J 634 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8222 (ttp-170) REVERT: J 635 HIS cc_start: 0.8406 (m90) cc_final: 0.7972 (m90) REVERT: K 303 MET cc_start: 0.8016 (tpp) cc_final: 0.7708 (ttm) REVERT: K 307 GLN cc_start: 0.8938 (tp40) cc_final: 0.8699 (tp-100) REVERT: K 308 GLU cc_start: 0.8925 (tt0) cc_final: 0.8706 (tp30) REVERT: K 412 MET cc_start: 0.8316 (mtp) cc_final: 0.8038 (mmt) REVERT: K 492 GLU cc_start: 0.8993 (tp30) cc_final: 0.8719 (tt0) REVERT: K 533 GLN cc_start: 0.8901 (mt0) cc_final: 0.8610 (tt0) REVERT: K 573 GLU cc_start: 0.8776 (tt0) cc_final: 0.8485 (mt-10) REVERT: K 619 ASP cc_start: 0.8598 (m-30) cc_final: 0.8290 (t70) REVERT: K 634 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.8328 (ttp-170) REVERT: L 303 MET cc_start: 0.8177 (tpp) cc_final: 0.7853 (ttm) REVERT: L 308 GLU cc_start: 0.8868 (tt0) cc_final: 0.8520 (tp30) REVERT: L 329 MET cc_start: 0.9089 (ttp) cc_final: 0.8870 (ttp) REVERT: L 412 MET cc_start: 0.8210 (mtp) cc_final: 0.7829 (mmt) REVERT: L 492 GLU cc_start: 0.8738 (tp30) cc_final: 0.8494 (tt0) REVERT: L 533 GLN cc_start: 0.8723 (mt0) cc_final: 0.8511 (tt0) REVERT: L 573 GLU cc_start: 0.8916 (tt0) cc_final: 0.8593 (mt-10) REVERT: L 590 MET cc_start: 0.8379 (ttm) cc_final: 0.8138 (tmm) REVERT: L 619 ASP cc_start: 0.8841 (m-30) cc_final: 0.8605 (t0) REVERT: L 634 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8260 (ttp-170) REVERT: L 635 HIS cc_start: 0.8396 (m90) cc_final: 0.7927 (m90) REVERT: M 303 MET cc_start: 0.8268 (tpp) cc_final: 0.7938 (ttm) REVERT: M 308 GLU cc_start: 0.8640 (tt0) cc_final: 0.8274 (tp30) REVERT: M 412 MET cc_start: 0.8328 (mtp) cc_final: 0.8047 (mpp) REVERT: M 533 GLN cc_start: 0.8615 (mt0) cc_final: 0.8323 (tt0) REVERT: M 573 GLU cc_start: 0.8807 (tt0) cc_final: 0.8475 (mt-10) REVERT: M 590 MET cc_start: 0.8248 (ttm) cc_final: 0.8011 (tmm) REVERT: M 619 ASP cc_start: 0.8533 (m-30) cc_final: 0.8231 (t70) REVERT: M 634 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.8281 (ttp-170) REVERT: M 635 HIS cc_start: 0.8446 (m90) cc_final: 0.8182 (m90) REVERT: N 307 GLN cc_start: 0.8788 (tp40) cc_final: 0.8557 (tp-100) REVERT: N 329 MET cc_start: 0.9069 (ttp) cc_final: 0.8867 (ttp) REVERT: N 412 MET cc_start: 0.8146 (mtp) cc_final: 0.7794 (mmp) REVERT: N 492 GLU cc_start: 0.8778 (tp30) cc_final: 0.8454 (tt0) REVERT: N 533 GLN cc_start: 0.8779 (mt0) cc_final: 0.8561 (tt0) REVERT: N 590 MET cc_start: 0.8483 (ttm) cc_final: 0.8247 (tmm) REVERT: N 619 ASP cc_start: 0.8638 (m-30) cc_final: 0.8383 (t0) REVERT: O 252 GLU cc_start: 0.9393 (tp30) cc_final: 0.8955 (pt0) REVERT: O 303 MET cc_start: 0.7954 (tpp) cc_final: 0.7614 (ttm) REVERT: O 308 GLU cc_start: 0.8728 (tt0) cc_final: 0.8486 (tp30) REVERT: O 412 MET cc_start: 0.8315 (mtp) cc_final: 0.7987 (mmt) REVERT: O 492 GLU cc_start: 0.8769 (tp30) cc_final: 0.8439 (tt0) REVERT: O 501 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8589 (tm-30) REVERT: O 533 GLN cc_start: 0.8617 (mt0) cc_final: 0.8381 (tt0) REVERT: O 573 GLU cc_start: 0.8792 (tt0) cc_final: 0.8496 (mt-10) REVERT: O 590 MET cc_start: 0.8246 (ttm) cc_final: 0.7991 (tmm) REVERT: O 619 ASP cc_start: 0.8629 (m-30) cc_final: 0.8332 (t70) REVERT: O 633 LYS cc_start: 0.7631 (tppt) cc_final: 0.7356 (tppt) REVERT: O 635 HIS cc_start: 0.8279 (m90) cc_final: 0.8014 (m90) outliers start: 45 outliers final: 18 residues processed: 1391 average time/residue: 0.5679 time to fit residues: 1297.8059 Evaluate side-chains 875 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 853 time to evaluate : 4.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain F residue 522 GLN Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 522 GLN Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain I residue 235 MET Chi-restraints excluded: chain J residue 235 MET Chi-restraints excluded: chain J residue 522 GLN Chi-restraints excluded: chain K residue 235 MET Chi-restraints excluded: chain L residue 235 MET Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 522 GLN Chi-restraints excluded: chain N residue 235 MET Chi-restraints excluded: chain N residue 238 LYS Chi-restraints excluded: chain O residue 235 MET 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: 0.9990 chunk 309 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 375 optimal weight: 0.5980 chunk 297 optimal weight: 8.9990 chunk 576 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 350 optimal weight: 0.3980 chunk 428 optimal weight: 0.7980 chunk 667 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 241 ASN ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 241 ASN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 266 GLN 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 266 GLN ** 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** I 132 HIS I 241 ASN ** I 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 445 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 K 241 ASN ** K 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 GLN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 HIS ** L 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 132 HIS M 241 ASN ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 241 ASN N 264 ASN 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** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 57015 Z= 0.263 Angle : 0.707 8.536 77175 Z= 0.371 Chirality : 0.049 0.210 9420 Planarity : 0.006 0.105 10065 Dihedral : 6.221 48.191 7942 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.01 % Favored : 93.79 % Rotamer: Outliers : 2.05 % Allowed : 11.63 % Favored : 86.33 % 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: -3.34 (0.09), residues: 7290 helix: -1.39 (0.10), residues: 2280 sheet: -2.51 (0.09), residues: 2580 loop : -2.29 (0.11), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 341 HIS 0.006 0.001 HIS C 132 PHE 0.014 0.002 PHE G 642 TYR 0.020 0.002 TYR D 133 ARG 0.007 0.001 ARG N 226 *********************** 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 1259 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1132 time to evaluate : 4.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.7798 (tpp) cc_final: 0.7356 (ttm) REVERT: A 412 MET cc_start: 0.8192 (mtp) cc_final: 0.7936 (mmp) REVERT: A 492 GLU cc_start: 0.8649 (tp30) cc_final: 0.8270 (tt0) REVERT: A 501 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8330 (tm-30) REVERT: A 533 GLN cc_start: 0.8645 (mt0) cc_final: 0.8433 (tt0) REVERT: A 590 MET cc_start: 0.8374 (ttm) cc_final: 0.8117 (tmm) REVERT: A 619 ASP cc_start: 0.8664 (m-30) cc_final: 0.8393 (t70) REVERT: A 633 LYS cc_start: 0.7069 (tppt) cc_final: 0.6775 (tptt) REVERT: B 303 MET cc_start: 0.8135 (tpp) cc_final: 0.7789 (ttm) REVERT: B 308 GLU cc_start: 0.8832 (tt0) cc_final: 0.8323 (tp30) REVERT: B 312 GLN cc_start: 0.8582 (mt0) cc_final: 0.8264 (mt0) REVERT: B 412 MET cc_start: 0.8297 (mtp) cc_final: 0.8030 (mmt) REVERT: B 444 ASP cc_start: 0.7718 (m-30) cc_final: 0.7400 (t0) REVERT: B 492 GLU cc_start: 0.8706 (tp30) cc_final: 0.8401 (tt0) REVERT: B 501 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8469 (tm-30) REVERT: B 506 ASN cc_start: 0.8320 (t0) cc_final: 0.8095 (t0) REVERT: B 573 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8648 (mt-10) REVERT: B 588 ASP cc_start: 0.8346 (m-30) cc_final: 0.8134 (p0) REVERT: B 619 ASP cc_start: 0.8513 (m-30) cc_final: 0.8231 (t0) REVERT: C 412 MET cc_start: 0.8408 (mtp) cc_final: 0.7913 (mmp) REVERT: C 492 GLU cc_start: 0.8671 (tp30) cc_final: 0.8247 (tt0) REVERT: C 506 ASN cc_start: 0.8312 (t0) cc_final: 0.8068 (t0) REVERT: C 533 GLN cc_start: 0.8742 (mt0) cc_final: 0.8517 (tt0) REVERT: C 590 MET cc_start: 0.8136 (ttm) cc_final: 0.7837 (tmm) REVERT: C 619 ASP cc_start: 0.8662 (m-30) cc_final: 0.8415 (t70) REVERT: D 412 MET cc_start: 0.8320 (mtp) cc_final: 0.8018 (mmp) REVERT: D 445 ASN cc_start: 0.8362 (m-40) cc_final: 0.8127 (m110) REVERT: D 492 GLU cc_start: 0.8682 (tp30) cc_final: 0.8379 (tt0) REVERT: D 501 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8196 (tm-30) REVERT: D 522 GLN cc_start: 0.9018 (tt0) cc_final: 0.8772 (tt0) REVERT: D 573 GLU cc_start: 0.9068 (tt0) cc_final: 0.8816 (mt-10) REVERT: D 619 ASP cc_start: 0.8427 (m-30) cc_final: 0.8133 (t0) REVERT: E 303 MET cc_start: 0.8394 (tpp) cc_final: 0.8160 (tpp) REVERT: E 308 GLU cc_start: 0.8706 (tt0) cc_final: 0.8442 (tp30) REVERT: E 492 GLU cc_start: 0.8474 (tp30) cc_final: 0.8145 (tt0) REVERT: E 501 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8336 (tm-30) REVERT: E 534 MET cc_start: 0.9025 (ttp) cc_final: 0.8704 (ttp) REVERT: E 619 ASP cc_start: 0.8539 (m-30) cc_final: 0.7943 (t70) REVERT: E 622 HIS cc_start: 0.8524 (m170) cc_final: 0.8294 (m170) REVERT: F 303 MET cc_start: 0.8284 (tpp) cc_final: 0.8030 (ttm) REVERT: F 412 MET cc_start: 0.8093 (mtp) cc_final: 0.7832 (mmp) REVERT: F 492 GLU cc_start: 0.8769 (tp30) cc_final: 0.8490 (tt0) REVERT: F 501 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8223 (tm-30) REVERT: F 590 MET cc_start: 0.8432 (ttm) cc_final: 0.8174 (tmm) REVERT: F 619 ASP cc_start: 0.8552 (m-30) cc_final: 0.8281 (t0) REVERT: G 312 GLN cc_start: 0.8888 (mt0) cc_final: 0.8644 (mt0) REVERT: G 412 MET cc_start: 0.8392 (mtp) cc_final: 0.8050 (mmp) REVERT: G 492 GLU cc_start: 0.8763 (tp30) cc_final: 0.8386 (tt0) REVERT: G 522 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8718 (tt0) REVERT: G 619 ASP cc_start: 0.8746 (m-30) cc_final: 0.8450 (t0) REVERT: H 303 MET cc_start: 0.8278 (tpp) cc_final: 0.7855 (ttm) REVERT: H 412 MET cc_start: 0.8329 (mtp) cc_final: 0.7967 (mmp) REVERT: H 492 GLU cc_start: 0.8727 (tp30) cc_final: 0.8413 (tt0) REVERT: H 506 ASN cc_start: 0.8258 (t0) cc_final: 0.8017 (t0) REVERT: H 533 GLN cc_start: 0.8602 (mt0) cc_final: 0.8376 (tt0) REVERT: H 618 MET cc_start: 0.8288 (mtp) cc_final: 0.8035 (mtp) REVERT: H 619 ASP cc_start: 0.8771 (m-30) cc_final: 0.8515 (t70) REVERT: I 303 MET cc_start: 0.8301 (tpp) cc_final: 0.7954 (ttm) REVERT: I 412 MET cc_start: 0.8219 (mtp) cc_final: 0.7957 (mmp) REVERT: I 492 GLU cc_start: 0.8519 (tp30) cc_final: 0.8195 (tt0) REVERT: I 501 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8289 (tm-30) REVERT: I 506 ASN cc_start: 0.8194 (t0) cc_final: 0.7987 (t0) REVERT: I 575 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8304 (ttmm) REVERT: I 619 ASP cc_start: 0.8561 (m-30) cc_final: 0.8290 (t70) REVERT: J 303 MET cc_start: 0.8241 (tpp) cc_final: 0.7931 (ttm) REVERT: J 412 MET cc_start: 0.8334 (mtp) cc_final: 0.8012 (mmp) REVERT: J 501 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8430 (tm-30) REVERT: J 522 GLN cc_start: 0.8957 (tt0) cc_final: 0.8627 (tt0) REVERT: J 618 MET cc_start: 0.8360 (mtp) cc_final: 0.8144 (mtp) REVERT: J 619 ASP cc_start: 0.8647 (m-30) cc_final: 0.8406 (t0) REVERT: K 303 MET cc_start: 0.8109 (tpp) cc_final: 0.7814 (ttm) REVERT: K 412 MET cc_start: 0.8226 (mtp) cc_final: 0.7922 (mmp) REVERT: K 492 GLU cc_start: 0.8587 (tp30) cc_final: 0.8264 (tt0) REVERT: K 501 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8292 (tm-30) REVERT: K 533 GLN cc_start: 0.8730 (mt0) cc_final: 0.8529 (tt0) REVERT: K 573 GLU cc_start: 0.8944 (tt0) cc_final: 0.8659 (mt-10) REVERT: K 619 ASP cc_start: 0.8591 (m-30) cc_final: 0.8359 (t70) REVERT: L 303 MET cc_start: 0.8265 (tpp) cc_final: 0.7840 (ttm) REVERT: L 412 MET cc_start: 0.8194 (mtp) cc_final: 0.7943 (mmp) REVERT: L 492 GLU cc_start: 0.8603 (tp30) cc_final: 0.8266 (tt0) REVERT: L 501 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8109 (tm-30) REVERT: L 573 GLU cc_start: 0.8962 (tt0) cc_final: 0.8670 (mt-10) REVERT: L 619 ASP cc_start: 0.8716 (m-30) cc_final: 0.8497 (t0) REVERT: M 235 MET cc_start: 0.5328 (mpp) cc_final: 0.5065 (mpp) REVERT: M 252 GLU cc_start: 0.9076 (tp30) cc_final: 0.8855 (pt0) REVERT: M 303 MET cc_start: 0.8341 (tpp) cc_final: 0.8021 (ttm) REVERT: M 308 GLU cc_start: 0.8609 (tt0) cc_final: 0.8374 (tp30) REVERT: M 412 MET cc_start: 0.8335 (mtp) cc_final: 0.7970 (mmp) REVERT: M 533 GLN cc_start: 0.8625 (mt0) cc_final: 0.8329 (tt0) REVERT: M 573 GLU cc_start: 0.9034 (tt0) cc_final: 0.8735 (mt-10) REVERT: M 619 ASP cc_start: 0.8582 (m-30) cc_final: 0.8301 (t0) REVERT: N 303 MET cc_start: 0.8172 (tpt) cc_final: 0.7821 (tpp) REVERT: N 312 GLN cc_start: 0.8766 (mt0) cc_final: 0.8454 (mt0) REVERT: N 412 MET cc_start: 0.8371 (mtp) cc_final: 0.7948 (mmp) REVERT: N 444 ASP cc_start: 0.8258 (m-30) cc_final: 0.7907 (t0) REVERT: N 492 GLU cc_start: 0.8662 (tp30) cc_final: 0.8338 (tt0) REVERT: N 501 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8253 (tm-30) REVERT: N 533 GLN cc_start: 0.8666 (mt0) cc_final: 0.8459 (tt0) REVERT: N 590 MET cc_start: 0.8404 (ttm) cc_final: 0.8182 (tmm) REVERT: N 619 ASP cc_start: 0.8569 (m-30) cc_final: 0.8290 (t0) REVERT: O 241 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7920 (m-40) REVERT: O 308 GLU cc_start: 0.8695 (tt0) cc_final: 0.8445 (tp30) REVERT: O 312 GLN cc_start: 0.8671 (mt0) cc_final: 0.8433 (mt0) REVERT: O 412 MET cc_start: 0.8374 (mtp) cc_final: 0.7978 (mmp) REVERT: O 445 ASN cc_start: 0.8663 (m110) cc_final: 0.8454 (m110) REVERT: O 492 GLU cc_start: 0.8551 (tp30) cc_final: 0.8223 (tt0) REVERT: O 619 ASP cc_start: 0.8725 (m-30) cc_final: 0.8461 (t0) outliers start: 127 outliers final: 35 residues processed: 1209 average time/residue: 0.4958 time to fit residues: 1039.0530 Evaluate side-chains 913 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 876 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain G residue 241 ASN Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 520 LYS Chi-restraints excluded: chain G residue 522 GLN Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 241 ASN Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain K residue 241 ASN Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain M residue 241 ASN Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain N residue 323 GLU Chi-restraints excluded: chain O residue 241 ASN Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 253 ASP Chi-restraints excluded: chain O residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 555 optimal weight: 1.9990 chunk 454 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 668 optimal weight: 0.8980 chunk 722 optimal weight: 1.9990 chunk 595 optimal weight: 20.0000 chunk 663 optimal weight: 0.6980 chunk 227 optimal weight: 4.9990 chunk 536 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 445 ASN A 502 GLN B 241 ASN B 264 ASN B 288 HIS B 408 ASN B 502 GLN C 264 ASN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 408 ASN D 502 GLN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 HIS ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 GLN F 264 ASN F 288 HIS ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 502 GLN G 264 ASN G 408 ASN G 502 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 HIS ** H 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 ASN I 288 HIS ** 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 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 408 ASN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 GLN K 288 HIS ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 408 ASN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 288 HIS M 312 GLN ** M 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 ASN M 445 ASN M 502 GLN M 524 ASN ** N 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 57015 Z= 0.269 Angle : 0.636 7.066 77175 Z= 0.322 Chirality : 0.047 0.206 9420 Planarity : 0.006 0.102 10065 Dihedral : 5.154 61.340 7878 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.05 % Favored : 93.74 % Rotamer: Outliers : 3.24 % Allowed : 13.41 % Favored : 83.35 % 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: -2.66 (0.09), residues: 7290 helix: -0.53 (0.10), residues: 2355 sheet: -2.30 (0.09), residues: 2685 loop : -1.99 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 341 HIS 0.005 0.001 HIS H 635 PHE 0.009 0.001 PHE G 642 TYR 0.020 0.002 TYR A 133 ARG 0.008 0.000 ARG G 226 *********************** 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 1098 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 897 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8019 (tpp) cc_final: 0.7639 (ttm) REVERT: A 312 GLN cc_start: 0.8635 (mt0) cc_final: 0.8090 (mt0) REVERT: A 412 MET cc_start: 0.8127 (mtp) cc_final: 0.7893 (mmp) REVERT: A 445 ASN cc_start: 0.8527 (m-40) cc_final: 0.8259 (m110) REVERT: A 492 GLU cc_start: 0.8720 (tp30) cc_final: 0.8388 (tt0) REVERT: A 501 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8615 (mp0) REVERT: A 533 GLN cc_start: 0.8656 (mt0) cc_final: 0.8437 (tt0) REVERT: A 619 ASP cc_start: 0.8639 (m-30) cc_final: 0.8398 (t70) REVERT: A 620 ASP cc_start: 0.8524 (m-30) cc_final: 0.7771 (p0) REVERT: A 633 LYS cc_start: 0.7207 (tppt) cc_final: 0.6898 (tptt) REVERT: B 303 MET cc_start: 0.8147 (tpp) cc_final: 0.7894 (tpp) REVERT: B 412 MET cc_start: 0.8252 (mtp) cc_final: 0.8015 (mmt) REVERT: B 492 GLU cc_start: 0.8827 (tp30) cc_final: 0.8559 (tt0) REVERT: B 501 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8592 (tm-30) REVERT: B 506 ASN cc_start: 0.8248 (t0) cc_final: 0.7639 (p0) REVERT: B 619 ASP cc_start: 0.8358 (m-30) cc_final: 0.7920 (t70) REVERT: B 622 HIS cc_start: 0.8791 (m170) cc_final: 0.8578 (m170) REVERT: C 312 GLN cc_start: 0.8647 (mt0) cc_final: 0.8160 (mt0) REVERT: C 412 MET cc_start: 0.8313 (mtp) cc_final: 0.7856 (mmp) REVERT: C 492 GLU cc_start: 0.8751 (tp30) cc_final: 0.8470 (tt0) REVERT: C 501 GLU cc_start: 0.8402 (mp0) cc_final: 0.8097 (tm-30) REVERT: C 533 GLN cc_start: 0.8622 (mt0) cc_final: 0.8415 (tt0) REVERT: C 590 MET cc_start: 0.8278 (ttm) cc_final: 0.7975 (tmm) REVERT: C 619 ASP cc_start: 0.8609 (m-30) cc_final: 0.8389 (t70) REVERT: D 308 GLU cc_start: 0.8767 (tp30) cc_final: 0.8489 (tp30) REVERT: D 312 GLN cc_start: 0.8929 (mt0) cc_final: 0.8676 (mt0) REVERT: D 412 MET cc_start: 0.8261 (mtp) cc_final: 0.7975 (mmp) REVERT: D 492 GLU cc_start: 0.8724 (tp30) cc_final: 0.8371 (tt0) REVERT: D 501 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8425 (tm-30) REVERT: D 522 GLN cc_start: 0.9068 (tt0) cc_final: 0.8679 (tt0) REVERT: D 573 GLU cc_start: 0.9044 (tt0) cc_final: 0.8788 (mt-10) REVERT: D 619 ASP cc_start: 0.8411 (m-30) cc_final: 0.8138 (t0) REVERT: E 241 ASN cc_start: 0.8065 (p0) cc_final: 0.7748 (m-40) REVERT: E 303 MET cc_start: 0.8414 (tpp) cc_final: 0.8181 (tpp) REVERT: E 308 GLU cc_start: 0.8730 (tt0) cc_final: 0.8510 (tp30) REVERT: E 314 ASP cc_start: 0.8373 (t0) cc_final: 0.8149 (t0) REVERT: E 492 GLU cc_start: 0.8530 (tp30) cc_final: 0.8202 (tt0) REVERT: E 501 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8446 (tm-30) REVERT: E 534 MET cc_start: 0.9072 (ttp) cc_final: 0.8855 (ttp) REVERT: E 619 ASP cc_start: 0.8308 (m-30) cc_final: 0.7891 (t70) REVERT: E 622 HIS cc_start: 0.8549 (m170) cc_final: 0.8287 (m170) REVERT: F 303 MET cc_start: 0.8127 (tpp) cc_final: 0.7904 (mmm) REVERT: F 412 MET cc_start: 0.8106 (mtp) cc_final: 0.7864 (mmp) REVERT: F 492 GLU cc_start: 0.8801 (tp30) cc_final: 0.8516 (tt0) REVERT: F 590 MET cc_start: 0.8340 (ttm) cc_final: 0.8113 (tmm) REVERT: F 619 ASP cc_start: 0.8422 (m-30) cc_final: 0.8139 (t0) REVERT: G 308 GLU cc_start: 0.8830 (tp30) cc_final: 0.8527 (mt-10) REVERT: G 312 GLN cc_start: 0.8887 (mt0) cc_final: 0.8676 (mt0) REVERT: G 412 MET cc_start: 0.8341 (mtp) cc_final: 0.7843 (mmp) REVERT: G 492 GLU cc_start: 0.8799 (tp30) cc_final: 0.8478 (tt0) REVERT: G 522 GLN cc_start: 0.9126 (tt0) cc_final: 0.8510 (tt0) REVERT: G 619 ASP cc_start: 0.8609 (m-30) cc_final: 0.8295 (t0) REVERT: H 241 ASN cc_start: 0.8256 (p0) cc_final: 0.7973 (m110) REVERT: H 308 GLU cc_start: 0.8813 (tp30) cc_final: 0.8496 (tp30) REVERT: H 312 GLN cc_start: 0.8897 (mt0) cc_final: 0.8603 (mt0) REVERT: H 412 MET cc_start: 0.7939 (mtp) cc_final: 0.7646 (mmp) REVERT: H 492 GLU cc_start: 0.8719 (tp30) cc_final: 0.8412 (tt0) REVERT: H 506 ASN cc_start: 0.8282 (t0) cc_final: 0.8049 (t0) REVERT: H 533 GLN cc_start: 0.8620 (mt0) cc_final: 0.8381 (tt0) REVERT: H 618 MET cc_start: 0.8205 (mtp) cc_final: 0.7918 (mtp) REVERT: H 619 ASP cc_start: 0.8606 (m-30) cc_final: 0.8342 (t70) REVERT: I 308 GLU cc_start: 0.8685 (tp30) cc_final: 0.8211 (tp30) REVERT: I 312 GLN cc_start: 0.8725 (mt0) cc_final: 0.8102 (mt0) REVERT: I 412 MET cc_start: 0.8183 (mtp) cc_final: 0.7925 (mmp) REVERT: I 492 GLU cc_start: 0.8623 (tp30) cc_final: 0.8321 (tt0) REVERT: I 501 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8355 (tm-30) REVERT: I 590 MET cc_start: 0.8559 (tpp) cc_final: 0.8255 (tmm) REVERT: I 619 ASP cc_start: 0.8514 (m-30) cc_final: 0.8276 (t0) REVERT: J 265 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7769 (tt) REVERT: J 303 MET cc_start: 0.8344 (tpp) cc_final: 0.7859 (mtp) REVERT: J 412 MET cc_start: 0.8263 (mtp) cc_final: 0.7863 (mmp) REVERT: J 501 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8487 (tm-30) REVERT: J 618 MET cc_start: 0.8460 (mtp) cc_final: 0.8168 (mtp) REVERT: J 619 ASP cc_start: 0.8558 (m-30) cc_final: 0.8317 (t0) REVERT: K 303 MET cc_start: 0.8098 (tpp) cc_final: 0.7870 (tpp) REVERT: K 314 ASP cc_start: 0.8045 (t0) cc_final: 0.7604 (t0) REVERT: K 412 MET cc_start: 0.8147 (mtp) cc_final: 0.7810 (mmp) REVERT: K 492 GLU cc_start: 0.8712 (tp30) cc_final: 0.8411 (tt0) REVERT: K 501 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8349 (tm-30) REVERT: K 522 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8777 (tt0) REVERT: K 573 GLU cc_start: 0.8933 (tt0) cc_final: 0.8630 (mt-10) REVERT: K 619 ASP cc_start: 0.8322 (m-30) cc_final: 0.8019 (t70) REVERT: L 303 MET cc_start: 0.8296 (tpp) cc_final: 0.7749 (mtp) REVERT: L 412 MET cc_start: 0.8105 (mtp) cc_final: 0.7671 (mmp) REVERT: L 492 GLU cc_start: 0.8518 (tp30) cc_final: 0.8226 (tt0) REVERT: L 501 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8144 (tm-30) REVERT: L 573 GLU cc_start: 0.8904 (tt0) cc_final: 0.8590 (mt-10) REVERT: L 619 ASP cc_start: 0.8446 (m-30) cc_final: 0.8207 (t0) REVERT: M 252 GLU cc_start: 0.9050 (tp30) cc_final: 0.8786 (pt0) REVERT: M 303 MET cc_start: 0.8259 (tpp) cc_final: 0.7954 (ttm) REVERT: M 308 GLU cc_start: 0.8697 (tt0) cc_final: 0.8458 (tp30) REVERT: M 412 MET cc_start: 0.8310 (mtp) cc_final: 0.7935 (mmp) REVERT: M 501 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7923 (mp0) REVERT: M 533 GLN cc_start: 0.8664 (mt0) cc_final: 0.8388 (tt0) REVERT: M 573 GLU cc_start: 0.9000 (tt0) cc_final: 0.8693 (mt-10) REVERT: M 619 ASP cc_start: 0.8413 (m-30) cc_final: 0.8145 (t0) REVERT: N 412 MET cc_start: 0.8330 (mtp) cc_final: 0.8054 (mmp) REVERT: N 492 GLU cc_start: 0.8749 (tp30) cc_final: 0.8431 (tt0) REVERT: N 501 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8333 (tm-30) REVERT: N 533 GLN cc_start: 0.8642 (mt0) cc_final: 0.8400 (tt0) REVERT: N 590 MET cc_start: 0.8307 (ttm) cc_final: 0.8017 (tmm) REVERT: N 619 ASP cc_start: 0.8511 (m-30) cc_final: 0.8262 (t0) REVERT: O 412 MET cc_start: 0.8163 (mtp) cc_final: 0.7782 (mmp) REVERT: O 445 ASN cc_start: 0.8599 (m110) cc_final: 0.8379 (m-40) REVERT: O 492 GLU cc_start: 0.8665 (tp30) cc_final: 0.8342 (tt0) REVERT: O 590 MET cc_start: 0.8115 (ttm) cc_final: 0.7825 (tmm) REVERT: O 595 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8511 (tp) REVERT: O 606 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8481 (mm-30) REVERT: O 619 ASP cc_start: 0.8491 (m-30) cc_final: 0.8221 (t0) outliers start: 201 outliers final: 100 residues processed: 1037 average time/residue: 0.4874 time to fit residues: 879.2342 Evaluate side-chains 877 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 774 time to evaluate : 4.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 415 VAL Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 520 LYS Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 623 ILE Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain I residue 511 ASN Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 643 ILE Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 522 GLN Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain L residue 363 MET Chi-restraints excluded: chain L residue 415 VAL Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 522 GLN Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 323 GLU Chi-restraints excluded: chain M residue 363 MET Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 595 ILE Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 323 GLU Chi-restraints excluded: chain N residue 363 MET Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 520 LYS Chi-restraints excluded: chain N residue 522 GLN Chi-restraints excluded: chain N residue 534 MET Chi-restraints excluded: chain N residue 554 LEU Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 415 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 522 GLN Chi-restraints excluded: chain O residue 595 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 0.9990 chunk 502 optimal weight: 6.9990 chunk 347 optimal weight: 40.0000 chunk 74 optimal weight: 9.9990 chunk 319 optimal weight: 0.9980 chunk 449 optimal weight: 6.9990 chunk 671 optimal weight: 0.9980 chunk 710 optimal weight: 20.0000 chunk 350 optimal weight: 6.9990 chunk 636 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 288 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS D 288 HIS ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 ASN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN H 241 ASN H 408 ASN H 601 ASN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 HIS J 289 GLN J 408 ASN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 264 ASN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 ASN L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 HIS ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 57015 Z= 0.389 Angle : 0.664 7.323 77175 Z= 0.335 Chirality : 0.047 0.232 9420 Planarity : 0.006 0.097 10065 Dihedral : 5.017 21.249 7875 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.97 % Favored : 91.82 % Rotamer: Outliers : 4.83 % Allowed : 14.90 % Favored : 80.27 % 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: -2.41 (0.09), residues: 7290 helix: -0.18 (0.11), residues: 2355 sheet: -2.16 (0.09), residues: 2700 loop : -2.04 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 341 HIS 0.006 0.001 HIS G 635 PHE 0.012 0.002 PHE H 642 TYR 0.019 0.002 TYR G 352 ARG 0.009 0.001 ARG L 181 *********************** 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 1099 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 799 time to evaluate : 4.719 Fit side-chains revert: symmetry clash REVERT: A 303 MET cc_start: 0.8061 (tpp) cc_final: 0.7828 (tpp) REVERT: A 412 MET cc_start: 0.8045 (mtp) cc_final: 0.7781 (mmp) REVERT: A 445 ASN cc_start: 0.8556 (m-40) cc_final: 0.8204 (m110) REVERT: A 492 GLU cc_start: 0.8738 (tp30) cc_final: 0.8371 (tt0) REVERT: A 533 GLN cc_start: 0.8602 (mt0) cc_final: 0.8384 (tt0) REVERT: A 619 ASP cc_start: 0.8462 (m-30) cc_final: 0.8233 (t70) REVERT: A 633 LYS cc_start: 0.7380 (tppt) cc_final: 0.7088 (tptt) REVERT: B 308 GLU cc_start: 0.8734 (tp30) cc_final: 0.8512 (tp30) REVERT: B 312 GLN cc_start: 0.8764 (mt0) cc_final: 0.8463 (mt0) REVERT: B 492 GLU cc_start: 0.8896 (tp30) cc_final: 0.8626 (tt0) REVERT: B 501 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8744 (tm-30) REVERT: B 619 ASP cc_start: 0.8266 (m-30) cc_final: 0.8011 (t0) REVERT: C 412 MET cc_start: 0.8200 (mtp) cc_final: 0.7937 (mmp) REVERT: C 492 GLU cc_start: 0.8859 (tp30) cc_final: 0.8517 (tt0) REVERT: C 501 GLU cc_start: 0.8785 (mp0) cc_final: 0.8385 (tm-30) REVERT: C 590 MET cc_start: 0.8290 (ttm) cc_final: 0.7998 (tmm) REVERT: C 619 ASP cc_start: 0.8610 (m-30) cc_final: 0.8394 (t70) REVERT: D 308 GLU cc_start: 0.8758 (tp30) cc_final: 0.8546 (tp30) REVERT: D 312 GLN cc_start: 0.8967 (mt0) cc_final: 0.8708 (mt0) REVERT: D 314 ASP cc_start: 0.8404 (t0) cc_final: 0.8029 (t0) REVERT: D 327 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8789 (p) REVERT: D 412 MET cc_start: 0.8133 (mtp) cc_final: 0.7854 (mmp) REVERT: D 492 GLU cc_start: 0.8870 (tp30) cc_final: 0.8564 (tt0) REVERT: D 501 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8453 (tm-30) REVERT: D 573 GLU cc_start: 0.8996 (tt0) cc_final: 0.8706 (mt-10) REVERT: D 619 ASP cc_start: 0.8481 (m-30) cc_final: 0.8202 (t70) REVERT: E 308 GLU cc_start: 0.8803 (tt0) cc_final: 0.8585 (tp30) REVERT: E 314 ASP cc_start: 0.8547 (t0) cc_final: 0.8274 (t0) REVERT: E 492 GLU cc_start: 0.8653 (tp30) cc_final: 0.8376 (tt0) REVERT: E 501 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8573 (tm-30) REVERT: E 619 ASP cc_start: 0.8213 (m-30) cc_final: 0.8005 (t70) REVERT: F 303 MET cc_start: 0.8325 (tpp) cc_final: 0.8109 (ttm) REVERT: F 492 GLU cc_start: 0.8886 (tp30) cc_final: 0.8562 (tt0) REVERT: F 619 ASP cc_start: 0.8428 (m-30) cc_final: 0.8166 (t0) REVERT: G 412 MET cc_start: 0.8322 (mtp) cc_final: 0.8083 (mmp) REVERT: G 492 GLU cc_start: 0.8858 (tp30) cc_final: 0.8533 (tt0) REVERT: G 536 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8518 (p) REVERT: G 619 ASP cc_start: 0.8692 (m-30) cc_final: 0.8368 (t0) REVERT: H 412 MET cc_start: 0.7757 (mtp) cc_final: 0.7494 (mmp) REVERT: H 492 GLU cc_start: 0.8855 (tp30) cc_final: 0.8506 (tt0) REVERT: H 506 ASN cc_start: 0.8393 (t0) cc_final: 0.8169 (t0) REVERT: H 533 GLN cc_start: 0.8569 (mt0) cc_final: 0.8351 (tt0) REVERT: H 573 GLU cc_start: 0.9127 (tp30) cc_final: 0.8812 (mt-10) REVERT: H 618 MET cc_start: 0.8305 (mtp) cc_final: 0.8014 (mtp) REVERT: H 619 ASP cc_start: 0.8658 (m-30) cc_final: 0.8422 (t70) REVERT: I 303 MET cc_start: 0.8099 (mmm) cc_final: 0.7876 (tpp) REVERT: I 314 ASP cc_start: 0.8421 (t0) cc_final: 0.8043 (t0) REVERT: I 412 MET cc_start: 0.8133 (mtp) cc_final: 0.7904 (mmp) REVERT: I 492 GLU cc_start: 0.8781 (tp30) cc_final: 0.8431 (tt0) REVERT: I 501 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8550 (tm-30) REVERT: I 619 ASP cc_start: 0.8404 (m-30) cc_final: 0.8149 (t70) REVERT: J 132 HIS cc_start: 0.2478 (OUTLIER) cc_final: 0.2155 (t-90) REVERT: J 303 MET cc_start: 0.8362 (tpp) cc_final: 0.8139 (tpp) REVERT: J 412 MET cc_start: 0.8225 (mtp) cc_final: 0.7848 (mmp) REVERT: J 618 MET cc_start: 0.8435 (mtp) cc_final: 0.8176 (mtp) REVERT: J 619 ASP cc_start: 0.8583 (m-30) cc_final: 0.8359 (t0) REVERT: K 303 MET cc_start: 0.8206 (tpp) cc_final: 0.7979 (tpp) REVERT: K 314 ASP cc_start: 0.8564 (t0) cc_final: 0.8095 (t0) REVERT: K 412 MET cc_start: 0.8002 (mtp) cc_final: 0.7699 (mmp) REVERT: K 492 GLU cc_start: 0.8789 (tp30) cc_final: 0.8461 (tt0) REVERT: K 501 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8443 (tm-30) REVERT: K 573 GLU cc_start: 0.8882 (tt0) cc_final: 0.8589 (mt-10) REVERT: K 619 ASP cc_start: 0.8020 (m-30) cc_final: 0.7729 (t70) REVERT: L 303 MET cc_start: 0.8435 (tpp) cc_final: 0.8075 (tpp) REVERT: L 412 MET cc_start: 0.8041 (mtp) cc_final: 0.7727 (mmt) REVERT: L 492 GLU cc_start: 0.8716 (tp30) cc_final: 0.8467 (tt0) REVERT: L 501 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8455 (tm-30) REVERT: L 573 GLU cc_start: 0.8905 (tt0) cc_final: 0.8594 (mt-10) REVERT: L 619 ASP cc_start: 0.8339 (m-30) cc_final: 0.8073 (t0) REVERT: M 252 GLU cc_start: 0.9097 (tp30) cc_final: 0.8842 (pt0) REVERT: M 303 MET cc_start: 0.8365 (tpp) cc_final: 0.8054 (tpp) REVERT: M 308 GLU cc_start: 0.8679 (tt0) cc_final: 0.8459 (tp30) REVERT: M 445 ASN cc_start: 0.8846 (m-40) cc_final: 0.8628 (m110) REVERT: M 501 GLU cc_start: 0.8634 (tm-30) cc_final: 0.7951 (mp0) REVERT: M 533 GLN cc_start: 0.8616 (mt0) cc_final: 0.8337 (tt0) REVERT: M 573 GLU cc_start: 0.8949 (tt0) cc_final: 0.8627 (mt-10) REVERT: M 619 ASP cc_start: 0.8286 (m-30) cc_final: 0.8032 (t0) REVERT: N 312 GLN cc_start: 0.8700 (mt0) cc_final: 0.8465 (mt0) REVERT: N 412 MET cc_start: 0.8298 (mtp) cc_final: 0.8033 (mmp) REVERT: N 492 GLU cc_start: 0.8853 (tp30) cc_final: 0.8576 (tt0) REVERT: N 501 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8500 (tm-30) REVERT: N 533 GLN cc_start: 0.8562 (mt0) cc_final: 0.8310 (tt0) REVERT: N 590 MET cc_start: 0.8227 (ttm) cc_final: 0.7963 (tmm) REVERT: N 619 ASP cc_start: 0.8430 (m-30) cc_final: 0.8191 (t0) REVERT: O 241 ASN cc_start: 0.8302 (p0) cc_final: 0.8073 (m-40) REVERT: O 296 LEU cc_start: 0.8118 (mt) cc_final: 0.7813 (mt) REVERT: O 327 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8882 (p) REVERT: O 412 MET cc_start: 0.8068 (mtp) cc_final: 0.7772 (mmp) REVERT: O 492 GLU cc_start: 0.8759 (tp30) cc_final: 0.8404 (tt0) REVERT: O 506 ASN cc_start: 0.8425 (t0) cc_final: 0.8221 (t0) REVERT: O 573 GLU cc_start: 0.9044 (tp30) cc_final: 0.8689 (mt-10) REVERT: O 590 MET cc_start: 0.8072 (ttm) cc_final: 0.7799 (tmm) REVERT: O 606 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8298 (mm-30) REVERT: O 619 ASP cc_start: 0.8350 (m-30) cc_final: 0.8089 (t0) outliers start: 300 outliers final: 158 residues processed: 1018 average time/residue: 0.4941 time to fit residues: 881.6668 Evaluate side-chains 869 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 707 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 635 HIS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 635 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 449 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 623 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 511 ASN Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain J residue 132 HIS Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 323 GLU Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 408 ASN Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 485 LYS Chi-restraints excluded: chain J residue 520 LYS Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 635 HIS Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 522 GLN Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 635 HIS Chi-restraints excluded: chain L residue 323 GLU Chi-restraints excluded: chain L residue 363 MET Chi-restraints excluded: chain L residue 415 VAL Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 443 MET Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 522 GLN Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 537 LEU Chi-restraints excluded: chain L residue 554 LEU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 323 GLU Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 595 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 323 GLU Chi-restraints excluded: chain N residue 363 MET Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 522 GLN Chi-restraints excluded: chain N residue 534 MET Chi-restraints excluded: chain N residue 554 LEU Chi-restraints excluded: chain N residue 635 HIS Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 315 ILE Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 415 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 522 GLN Chi-restraints excluded: chain O residue 595 ILE Chi-restraints excluded: chain O residue 635 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 30.0000 chunk 403 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 528 optimal weight: 0.0970 chunk 293 optimal weight: 0.9990 chunk 606 optimal weight: 0.7980 chunk 491 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 362 optimal weight: 3.9990 chunk 637 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 GLN ** 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 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 576 ASN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 57015 Z= 0.219 Angle : 0.573 8.459 77175 Z= 0.290 Chirality : 0.046 0.203 9420 Planarity : 0.005 0.094 10065 Dihedral : 4.642 19.745 7875 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.88 % Favored : 94.91 % Rotamer: Outliers : 3.77 % Allowed : 17.31 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.10), residues: 7290 helix: 0.21 (0.11), residues: 2325 sheet: -2.05 (0.09), residues: 2670 loop : -1.64 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 341 HIS 0.004 0.001 HIS I 635 PHE 0.008 0.001 PHE O 642 TYR 0.017 0.001 TYR O 133 ARG 0.007 0.000 ARG H 181 *********************** 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 1019 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 785 time to evaluate : 4.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.7986 (tpp) cc_final: 0.7748 (tpp) REVERT: A 412 MET cc_start: 0.8200 (mtp) cc_final: 0.7954 (mmp) REVERT: A 445 ASN cc_start: 0.8382 (m-40) cc_final: 0.8023 (m110) REVERT: A 492 GLU cc_start: 0.8632 (tp30) cc_final: 0.8303 (tt0) REVERT: A 619 ASP cc_start: 0.8374 (m-30) cc_final: 0.8145 (t70) REVERT: A 620 ASP cc_start: 0.8547 (m-30) cc_final: 0.7822 (p0) REVERT: A 633 LYS cc_start: 0.7245 (tppt) cc_final: 0.6971 (tptt) REVERT: B 312 GLN cc_start: 0.8585 (mt0) cc_final: 0.8309 (mt0) REVERT: B 492 GLU cc_start: 0.8812 (tp30) cc_final: 0.8528 (tt0) REVERT: B 501 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8562 (tm-30) REVERT: B 619 ASP cc_start: 0.8145 (m-30) cc_final: 0.7865 (t0) REVERT: C 308 GLU cc_start: 0.8643 (tp30) cc_final: 0.8175 (tm-30) REVERT: C 412 MET cc_start: 0.8203 (mtp) cc_final: 0.7955 (mmp) REVERT: C 492 GLU cc_start: 0.8817 (tp30) cc_final: 0.8534 (tt0) REVERT: C 501 GLU cc_start: 0.8436 (mp0) cc_final: 0.8152 (tm-30) REVERT: C 619 ASP cc_start: 0.8571 (m-30) cc_final: 0.8337 (t70) REVERT: D 308 GLU cc_start: 0.8660 (tp30) cc_final: 0.8381 (tp30) REVERT: D 312 GLN cc_start: 0.8891 (mt0) cc_final: 0.8644 (mt0) REVERT: D 327 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8796 (p) REVERT: D 412 MET cc_start: 0.8133 (mtp) cc_final: 0.7836 (mmp) REVERT: D 492 GLU cc_start: 0.8777 (tp30) cc_final: 0.8489 (tt0) REVERT: D 506 ASN cc_start: 0.8292 (t0) cc_final: 0.7695 (p0) REVERT: D 573 GLU cc_start: 0.9033 (tt0) cc_final: 0.8751 (mt-10) REVERT: D 619 ASP cc_start: 0.8487 (m-30) cc_final: 0.8184 (t70) REVERT: E 314 ASP cc_start: 0.8367 (t0) cc_final: 0.8064 (t0) REVERT: E 492 GLU cc_start: 0.8612 (tp30) cc_final: 0.8255 (tt0) REVERT: E 501 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8419 (tm-30) REVERT: E 506 ASN cc_start: 0.8433 (t0) cc_final: 0.7795 (p0) REVERT: E 619 ASP cc_start: 0.8150 (m-30) cc_final: 0.7927 (t70) REVERT: F 241 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.6756 (p0) REVERT: F 492 GLU cc_start: 0.8791 (tp30) cc_final: 0.8485 (tt0) REVERT: F 506 ASN cc_start: 0.8359 (t0) cc_final: 0.7749 (p0) REVERT: F 619 ASP cc_start: 0.8338 (m-30) cc_final: 0.8096 (t0) REVERT: G 412 MET cc_start: 0.8328 (mtp) cc_final: 0.8037 (mmp) REVERT: G 492 GLU cc_start: 0.8799 (tp30) cc_final: 0.8485 (tt0) REVERT: G 536 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8526 (p) REVERT: G 619 ASP cc_start: 0.8551 (m-30) cc_final: 0.8228 (t0) REVERT: H 412 MET cc_start: 0.7838 (mtp) cc_final: 0.7602 (mmp) REVERT: H 492 GLU cc_start: 0.8745 (tp30) cc_final: 0.8432 (tt0) REVERT: H 506 ASN cc_start: 0.8301 (t0) cc_final: 0.8088 (t0) REVERT: H 573 GLU cc_start: 0.9125 (tp30) cc_final: 0.8830 (mt-10) REVERT: H 618 MET cc_start: 0.8174 (mtp) cc_final: 0.7862 (mtp) REVERT: H 619 ASP cc_start: 0.8703 (m-30) cc_final: 0.8476 (t70) REVERT: I 303 MET cc_start: 0.8111 (mmm) cc_final: 0.7833 (tpp) REVERT: I 312 GLN cc_start: 0.8762 (mt0) cc_final: 0.8551 (pt0) REVERT: I 412 MET cc_start: 0.8107 (mtp) cc_final: 0.7882 (mmp) REVERT: I 492 GLU cc_start: 0.8607 (tp30) cc_final: 0.8293 (tt0) REVERT: I 501 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8439 (tm-30) REVERT: I 619 ASP cc_start: 0.8224 (m-30) cc_final: 0.7982 (t70) REVERT: J 303 MET cc_start: 0.8393 (tpp) cc_final: 0.8143 (tpp) REVERT: J 412 MET cc_start: 0.8161 (mtp) cc_final: 0.7817 (mmp) REVERT: J 619 ASP cc_start: 0.8485 (m-30) cc_final: 0.8244 (t0) REVERT: K 314 ASP cc_start: 0.8241 (t0) cc_final: 0.7961 (t0) REVERT: K 412 MET cc_start: 0.8104 (mtp) cc_final: 0.7795 (mmp) REVERT: K 492 GLU cc_start: 0.8679 (tp30) cc_final: 0.8363 (tt0) REVERT: K 501 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8414 (tm-30) REVERT: K 573 GLU cc_start: 0.8887 (tt0) cc_final: 0.8592 (mt-10) REVERT: K 619 ASP cc_start: 0.8015 (m-30) cc_final: 0.7776 (t70) REVERT: L 132 HIS cc_start: 0.3396 (OUTLIER) cc_final: 0.2859 (t-90) REVERT: L 303 MET cc_start: 0.8345 (tpp) cc_final: 0.8087 (tpp) REVERT: L 412 MET cc_start: 0.8053 (mtp) cc_final: 0.7811 (mmp) REVERT: L 492 GLU cc_start: 0.8607 (tp30) cc_final: 0.8321 (tt0) REVERT: L 501 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8196 (tm-30) REVERT: L 573 GLU cc_start: 0.8911 (tt0) cc_final: 0.8605 (mt-10) REVERT: L 619 ASP cc_start: 0.8263 (m-30) cc_final: 0.7978 (t0) REVERT: M 132 HIS cc_start: 0.3001 (OUTLIER) cc_final: 0.2622 (t-90) REVERT: M 252 GLU cc_start: 0.8896 (tp30) cc_final: 0.8675 (pt0) REVERT: M 303 MET cc_start: 0.8354 (tpp) cc_final: 0.8054 (ttm) REVERT: M 308 GLU cc_start: 0.8630 (tt0) cc_final: 0.8390 (tp30) REVERT: M 501 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7779 (mp0) REVERT: M 533 GLN cc_start: 0.8606 (mt0) cc_final: 0.8370 (tt0) REVERT: M 573 GLU cc_start: 0.9013 (tt0) cc_final: 0.8708 (mt-10) REVERT: M 619 ASP cc_start: 0.8160 (m-30) cc_final: 0.7915 (t70) REVERT: M 620 ASP cc_start: 0.8408 (m-30) cc_final: 0.7713 (p0) REVERT: N 312 GLN cc_start: 0.8800 (mt0) cc_final: 0.8576 (mt0) REVERT: N 412 MET cc_start: 0.8286 (mtp) cc_final: 0.7992 (mmp) REVERT: N 492 GLU cc_start: 0.8691 (tp30) cc_final: 0.8371 (tt0) REVERT: N 501 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8369 (tm-30) REVERT: N 506 ASN cc_start: 0.8393 (t0) cc_final: 0.7980 (p0) REVERT: N 590 MET cc_start: 0.8267 (ttm) cc_final: 0.7999 (tmm) REVERT: N 609 TYR cc_start: 0.8666 (t80) cc_final: 0.8398 (t80) REVERT: N 619 ASP cc_start: 0.8182 (m-30) cc_final: 0.7938 (t70) REVERT: O 296 LEU cc_start: 0.7996 (mt) cc_final: 0.7637 (mt) REVERT: O 327 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8850 (p) REVERT: O 412 MET cc_start: 0.8136 (mtp) cc_final: 0.7834 (mmp) REVERT: O 492 GLU cc_start: 0.8658 (tp30) cc_final: 0.8328 (tt0) REVERT: O 573 GLU cc_start: 0.9025 (tp30) cc_final: 0.8683 (mt-10) REVERT: O 590 MET cc_start: 0.8116 (ttm) cc_final: 0.7857 (tmm) REVERT: O 606 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8361 (mm-30) REVERT: O 619 ASP cc_start: 0.8157 (m-30) cc_final: 0.7884 (t0) outliers start: 234 outliers final: 138 residues processed: 968 average time/residue: 0.5000 time to fit residues: 846.9742 Evaluate side-chains 840 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 696 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 132 HIS Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 511 ASN Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 554 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 323 GLU Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 408 ASN Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 522 GLN Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain L residue 132 HIS Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 363 MET Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 522 GLN Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 363 MET Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 323 GLU Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 534 MET Chi-restraints excluded: chain N residue 554 LEU Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 415 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 522 GLN Chi-restraints excluded: chain O residue 549 GLU Chi-restraints excluded: chain O residue 595 ILE 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: 8.9990 chunk 140 optimal weight: 5.9990 chunk 417 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 711 optimal weight: 9.9990 chunk 590 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 chunk 373 optimal weight: 0.8980 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN C 601 ASN D 601 ASN ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 ASN G 601 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 601 ASN O 601 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 57015 Z= 0.595 Angle : 0.770 9.050 77175 Z= 0.391 Chirality : 0.050 0.223 9420 Planarity : 0.007 0.094 10065 Dihedral : 5.288 23.036 7875 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.60 % Favored : 90.19 % Rotamer: Outliers : 5.23 % Allowed : 17.54 % Favored : 77.23 % 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: -2.43 (0.10), residues: 7290 helix: -0.05 (0.11), residues: 2280 sheet: -2.34 (0.09), residues: 2640 loop : -1.96 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 341 HIS 0.010 0.002 HIS J 622 PHE 0.013 0.002 PHE L 518 TYR 0.026 0.003 TYR E 352 ARG 0.009 0.001 ARG N 521 *********************** 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 1050 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 725 time to evaluate : 4.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8409 (tpp) cc_final: 0.8193 (tpp) REVERT: A 314 ASP cc_start: 0.8651 (t0) cc_final: 0.8392 (t0) REVERT: A 412 MET cc_start: 0.8056 (mtp) cc_final: 0.7843 (mmp) REVERT: A 445 ASN cc_start: 0.8595 (m-40) cc_final: 0.8249 (m110) REVERT: A 492 GLU cc_start: 0.8876 (tp30) cc_final: 0.8618 (tt0) REVERT: A 619 ASP cc_start: 0.8450 (m-30) cc_final: 0.8222 (t70) REVERT: B 132 HIS cc_start: 0.2942 (OUTLIER) cc_final: 0.2733 (t70) REVERT: B 312 GLN cc_start: 0.8764 (mt0) cc_final: 0.8506 (mt0) REVERT: B 314 ASP cc_start: 0.8592 (t0) cc_final: 0.8228 (t0) REVERT: B 412 MET cc_start: 0.8208 (mmp) cc_final: 0.7617 (mtm) REVERT: B 492 GLU cc_start: 0.9004 (tp30) cc_final: 0.8707 (tt0) REVERT: B 501 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8821 (tm-30) REVERT: B 619 ASP cc_start: 0.8587 (m-30) cc_final: 0.8348 (t0) REVERT: C 412 MET cc_start: 0.8187 (mtp) cc_final: 0.7914 (mmp) REVERT: C 492 GLU cc_start: 0.8936 (tp30) cc_final: 0.8607 (tt0) REVERT: C 501 GLU cc_start: 0.8837 (mp0) cc_final: 0.8405 (tm-30) REVERT: C 546 LEU cc_start: 0.9360 (mp) cc_final: 0.8974 (tp) REVERT: C 590 MET cc_start: 0.8237 (ttm) cc_final: 0.7958 (tmm) REVERT: C 619 ASP cc_start: 0.8528 (m-30) cc_final: 0.8289 (t70) REVERT: D 308 GLU cc_start: 0.8679 (tp30) cc_final: 0.8470 (tp30) REVERT: D 312 GLN cc_start: 0.8892 (mt0) cc_final: 0.8552 (mt0) REVERT: D 314 ASP cc_start: 0.8540 (t0) cc_final: 0.8260 (t0) REVERT: D 327 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8862 (p) REVERT: D 412 MET cc_start: 0.7951 (mtp) cc_final: 0.7686 (mmp) REVERT: D 492 GLU cc_start: 0.8892 (tp30) cc_final: 0.8600 (tt0) REVERT: D 573 GLU cc_start: 0.8989 (tt0) cc_final: 0.8682 (mt-10) REVERT: D 619 ASP cc_start: 0.8563 (m-30) cc_final: 0.8287 (t0) REVERT: E 132 HIS cc_start: 0.3378 (OUTLIER) cc_final: 0.3064 (t70) REVERT: E 133 TYR cc_start: 0.3873 (p90) cc_final: 0.3573 (p90) REVERT: E 314 ASP cc_start: 0.8688 (t0) cc_final: 0.8412 (t0) REVERT: E 492 GLU cc_start: 0.8789 (tp30) cc_final: 0.8502 (tt0) REVERT: E 501 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8673 (tm-30) REVERT: E 506 ASN cc_start: 0.8658 (t0) cc_final: 0.8047 (p0) REVERT: E 619 ASP cc_start: 0.8131 (m-30) cc_final: 0.7898 (t70) REVERT: F 132 HIS cc_start: 0.3227 (OUTLIER) cc_final: 0.2799 (t70) REVERT: F 133 TYR cc_start: 0.4105 (p90) cc_final: 0.3756 (p90) REVERT: F 314 ASP cc_start: 0.8500 (t0) cc_final: 0.8242 (t0) REVERT: F 492 GLU cc_start: 0.8935 (tp30) cc_final: 0.8682 (tt0) REVERT: F 619 ASP cc_start: 0.8510 (m-30) cc_final: 0.8252 (t0) REVERT: G 314 ASP cc_start: 0.8529 (t0) cc_final: 0.8181 (t0) REVERT: G 412 MET cc_start: 0.8047 (mtp) cc_final: 0.7786 (mmp) REVERT: G 492 GLU cc_start: 0.8945 (tp30) cc_final: 0.8642 (tt0) REVERT: G 506 ASN cc_start: 0.8340 (t0) cc_final: 0.8112 (t0) REVERT: G 619 ASP cc_start: 0.8740 (m-30) cc_final: 0.8438 (t0) REVERT: H 314 ASP cc_start: 0.8721 (t0) cc_final: 0.8453 (t0) REVERT: H 412 MET cc_start: 0.7730 (mtp) cc_final: 0.7464 (mmp) REVERT: H 492 GLU cc_start: 0.8852 (tp30) cc_final: 0.8543 (tt0) REVERT: H 618 MET cc_start: 0.8418 (mtp) cc_final: 0.8168 (mtp) REVERT: H 619 ASP cc_start: 0.8739 (m-30) cc_final: 0.8505 (t0) REVERT: I 303 MET cc_start: 0.8207 (mmm) cc_final: 0.8002 (tpp) REVERT: I 412 MET cc_start: 0.8097 (mtp) cc_final: 0.7835 (mmp) REVERT: I 492 GLU cc_start: 0.8864 (tp30) cc_final: 0.8551 (tt0) REVERT: I 619 ASP cc_start: 0.8152 (m-30) cc_final: 0.7895 (t70) REVERT: J 314 ASP cc_start: 0.8375 (t0) cc_final: 0.8099 (t0) REVERT: J 412 MET cc_start: 0.8245 (mtp) cc_final: 0.7926 (mmp) REVERT: J 619 ASP cc_start: 0.8496 (m-30) cc_final: 0.8276 (t0) REVERT: K 314 ASP cc_start: 0.8606 (t0) cc_final: 0.8386 (t0) REVERT: K 412 MET cc_start: 0.8196 (mtp) cc_final: 0.7864 (mmp) REVERT: K 492 GLU cc_start: 0.8869 (tp30) cc_final: 0.8597 (tt0) REVERT: K 573 GLU cc_start: 0.8873 (tt0) cc_final: 0.8564 (mt-10) REVERT: K 619 ASP cc_start: 0.7985 (m-30) cc_final: 0.7690 (t70) REVERT: L 303 MET cc_start: 0.8533 (tpp) cc_final: 0.8244 (tpp) REVERT: L 314 ASP cc_start: 0.8644 (t0) cc_final: 0.8325 (t0) REVERT: L 412 MET cc_start: 0.8081 (mtp) cc_final: 0.7819 (mmp) REVERT: L 492 GLU cc_start: 0.8836 (tp30) cc_final: 0.8528 (tt0) REVERT: L 531 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8125 (t70) REVERT: L 573 GLU cc_start: 0.8926 (tt0) cc_final: 0.8634 (mt-10) REVERT: L 619 ASP cc_start: 0.8490 (m-30) cc_final: 0.8259 (t0) REVERT: L 620 ASP cc_start: 0.8609 (m-30) cc_final: 0.8032 (p0) REVERT: M 252 GLU cc_start: 0.9074 (tp30) cc_final: 0.8774 (pt0) REVERT: M 303 MET cc_start: 0.8476 (tpp) cc_final: 0.7961 (ttm) REVERT: M 307 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8024 (mt0) REVERT: M 308 GLU cc_start: 0.8630 (tt0) cc_final: 0.8381 (tp30) REVERT: M 501 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8083 (mp0) REVERT: M 533 GLN cc_start: 0.8551 (mt0) cc_final: 0.8216 (tt0) REVERT: M 573 GLU cc_start: 0.8976 (tt0) cc_final: 0.8643 (mt-10) REVERT: M 613 GLN cc_start: 0.7702 (mt0) cc_final: 0.7155 (pp30) REVERT: M 619 ASP cc_start: 0.8160 (m-30) cc_final: 0.7930 (t0) REVERT: N 412 MET cc_start: 0.8234 (mtp) cc_final: 0.7854 (mmp) REVERT: N 492 GLU cc_start: 0.8908 (tp30) cc_final: 0.8601 (tt0) REVERT: N 501 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8603 (tm-30) REVERT: N 590 MET cc_start: 0.8185 (ttm) cc_final: 0.7945 (tmm) REVERT: N 613 GLN cc_start: 0.7937 (mt0) cc_final: 0.7406 (pp30) REVERT: N 619 ASP cc_start: 0.8254 (m-30) cc_final: 0.8022 (t70) REVERT: O 307 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8336 (mt0) REVERT: O 314 ASP cc_start: 0.8651 (t0) cc_final: 0.8413 (t0) REVERT: O 327 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8927 (p) REVERT: O 412 MET cc_start: 0.8065 (mtp) cc_final: 0.7836 (mmt) REVERT: O 492 GLU cc_start: 0.8805 (tp30) cc_final: 0.8519 (tt0) REVERT: O 506 ASN cc_start: 0.8635 (t0) cc_final: 0.8398 (t0) REVERT: O 573 GLU cc_start: 0.9025 (tp30) cc_final: 0.8691 (mt-10) REVERT: O 590 MET cc_start: 0.7999 (ttm) cc_final: 0.7750 (tmm) REVERT: O 619 ASP cc_start: 0.8331 (m-30) cc_final: 0.8057 (t0) outliers start: 325 outliers final: 220 residues processed: 988 average time/residue: 0.4708 time to fit residues: 822.7365 Evaluate side-chains 918 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 692 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 522 GLN Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 623 ILE Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 635 HIS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 132 HIS Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 415 VAL Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 449 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 505 SER Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 631 GLU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 420 THR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 533 GLN Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain H residue 623 ILE Chi-restraints excluded: chain H residue 635 HIS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 443 MET Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 511 ASN Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 323 GLU Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 623 ILE Chi-restraints excluded: chain J residue 635 HIS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 291 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 426 VAL Chi-restraints excluded: chain K residue 449 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain K residue 635 HIS Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 363 MET Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 415 VAL Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 531 ASP Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 537 LEU Chi-restraints excluded: chain L residue 554 LEU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain L residue 623 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 323 GLU Chi-restraints excluded: chain M residue 363 MET Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 415 VAL Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 480 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 534 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 323 GLU Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 443 MET Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 534 MET Chi-restraints excluded: chain N residue 554 LEU Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 603 ILE Chi-restraints excluded: chain N residue 635 HIS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 291 THR Chi-restraints excluded: chain O residue 315 ILE Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 415 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 522 GLN Chi-restraints excluded: chain O residue 549 GLU Chi-restraints excluded: chain O residue 595 ILE Chi-restraints excluded: chain O residue 603 ILE Chi-restraints excluded: chain O residue 635 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 405 optimal weight: 2.9990 chunk 519 optimal weight: 6.9990 chunk 402 optimal weight: 7.9990 chunk 598 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 chunk 708 optimal weight: 1.9990 chunk 443 optimal weight: 10.0000 chunk 431 optimal weight: 0.9990 chunk 327 optimal weight: 0.4980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 D 266 GLN F 576 ASN G 489 GLN G 576 ASN H 489 GLN ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN I 266 GLN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 240 ASN J 266 GLN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 489 GLN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 57015 Z= 0.240 Angle : 0.595 8.869 77175 Z= 0.303 Chirality : 0.046 0.283 9420 Planarity : 0.005 0.091 10065 Dihedral : 4.727 22.347 7875 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.03 % Favored : 94.76 % Rotamer: Outliers : 3.67 % Allowed : 19.32 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 7290 helix: 0.24 (0.11), residues: 2280 sheet: -2.38 (0.09), residues: 2805 loop : -1.50 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 419 HIS 0.004 0.001 HIS J 622 PHE 0.008 0.001 PHE D 642 TYR 0.020 0.001 TYR C 133 ARG 0.007 0.000 ARG N 544 *********************** 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 985 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 757 time to evaluate : 4.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8311 (tpp) cc_final: 0.8076 (tpp) REVERT: A 412 MET cc_start: 0.8079 (mtp) cc_final: 0.7848 (mmt) REVERT: A 445 ASN cc_start: 0.8406 (m-40) cc_final: 0.8062 (m110) REVERT: A 492 GLU cc_start: 0.8724 (tp30) cc_final: 0.8398 (tt0) REVERT: A 619 ASP cc_start: 0.8475 (m-30) cc_final: 0.8249 (t70) REVERT: A 620 ASP cc_start: 0.8574 (m-30) cc_final: 0.7761 (p0) REVERT: B 132 HIS cc_start: 0.3085 (OUTLIER) cc_final: 0.2766 (t70) REVERT: B 312 GLN cc_start: 0.8569 (mt0) cc_final: 0.8264 (mt0) REVERT: B 412 MET cc_start: 0.8077 (mmp) cc_final: 0.7538 (mtm) REVERT: B 492 GLU cc_start: 0.8791 (tp30) cc_final: 0.8507 (tt0) REVERT: B 619 ASP cc_start: 0.8045 (m-30) cc_final: 0.7783 (t0) REVERT: C 412 MET cc_start: 0.8174 (mtp) cc_final: 0.7926 (mmp) REVERT: C 492 GLU cc_start: 0.8851 (tp30) cc_final: 0.8528 (tt0) REVERT: C 501 GLU cc_start: 0.8416 (mp0) cc_final: 0.8138 (tm-30) REVERT: C 546 LEU cc_start: 0.9409 (mp) cc_final: 0.9114 (tt) REVERT: C 590 MET cc_start: 0.8238 (ttm) cc_final: 0.7954 (tmm) REVERT: C 609 TYR cc_start: 0.8783 (t80) cc_final: 0.8558 (t80) REVERT: C 619 ASP cc_start: 0.8521 (m-30) cc_final: 0.8275 (t70) REVERT: D 308 GLU cc_start: 0.8552 (tp30) cc_final: 0.8222 (mt-10) REVERT: D 312 GLN cc_start: 0.8869 (mt0) cc_final: 0.8613 (mt0) REVERT: D 327 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8851 (p) REVERT: D 412 MET cc_start: 0.8039 (mtp) cc_final: 0.7760 (mmp) REVERT: D 492 GLU cc_start: 0.8856 (tp30) cc_final: 0.8583 (tt0) REVERT: D 573 GLU cc_start: 0.8990 (tt0) cc_final: 0.8696 (mt-10) REVERT: D 619 ASP cc_start: 0.8466 (m-30) cc_final: 0.8152 (t0) REVERT: E 314 ASP cc_start: 0.8516 (t0) cc_final: 0.8217 (t0) REVERT: E 492 GLU cc_start: 0.8664 (tp30) cc_final: 0.8315 (tt0) REVERT: E 501 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8538 (tm-30) REVERT: E 506 ASN cc_start: 0.8469 (t0) cc_final: 0.7880 (p0) REVERT: E 619 ASP cc_start: 0.8096 (m-30) cc_final: 0.7875 (t70) REVERT: F 132 HIS cc_start: 0.3817 (OUTLIER) cc_final: 0.3460 (t70) REVERT: F 492 GLU cc_start: 0.8752 (tp30) cc_final: 0.8398 (tt0) REVERT: F 619 ASP cc_start: 0.8392 (m-30) cc_final: 0.8156 (t0) REVERT: G 132 HIS cc_start: 0.2946 (OUTLIER) cc_final: 0.2591 (t-90) REVERT: G 412 MET cc_start: 0.8086 (mtp) cc_final: 0.7830 (mmp) REVERT: G 492 GLU cc_start: 0.8888 (tp30) cc_final: 0.8579 (tt0) REVERT: G 619 ASP cc_start: 0.8714 (m-30) cc_final: 0.8410 (t70) REVERT: H 412 MET cc_start: 0.7836 (mtp) cc_final: 0.7576 (mmp) REVERT: H 492 GLU cc_start: 0.8836 (tp30) cc_final: 0.8533 (tt0) REVERT: H 506 ASN cc_start: 0.8306 (t0) cc_final: 0.8092 (t0) REVERT: H 531 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7954 (t70) REVERT: H 618 MET cc_start: 0.8185 (mtp) cc_final: 0.7873 (mtp) REVERT: H 619 ASP cc_start: 0.8687 (m-30) cc_final: 0.8471 (t0) REVERT: I 303 MET cc_start: 0.8109 (mmm) cc_final: 0.7908 (tpp) REVERT: I 412 MET cc_start: 0.8210 (mtp) cc_final: 0.7958 (mmp) REVERT: I 492 GLU cc_start: 0.8783 (tp30) cc_final: 0.8472 (tt0) REVERT: I 501 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8463 (tm-30) REVERT: I 619 ASP cc_start: 0.8109 (m-30) cc_final: 0.7877 (t70) REVERT: I 634 ARG cc_start: 0.8837 (ttm-80) cc_final: 0.8472 (ttp-170) REVERT: J 412 MET cc_start: 0.8257 (mtp) cc_final: 0.7950 (mmp) REVERT: J 619 ASP cc_start: 0.8163 (m-30) cc_final: 0.7940 (t0) REVERT: K 235 MET cc_start: 0.4240 (OUTLIER) cc_final: 0.3688 (mmp) REVERT: K 314 ASP cc_start: 0.8306 (t0) cc_final: 0.8017 (t0) REVERT: K 412 MET cc_start: 0.8145 (mtp) cc_final: 0.7841 (mmt) REVERT: K 492 GLU cc_start: 0.8697 (tp30) cc_final: 0.8397 (tt0) REVERT: K 501 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8404 (tm-30) REVERT: K 573 GLU cc_start: 0.8946 (tt0) cc_final: 0.8650 (mt-10) REVERT: K 619 ASP cc_start: 0.7781 (m-30) cc_final: 0.7523 (t70) REVERT: L 303 MET cc_start: 0.8389 (tpp) cc_final: 0.8070 (tpp) REVERT: L 314 ASP cc_start: 0.8510 (t0) cc_final: 0.8206 (t0) REVERT: L 412 MET cc_start: 0.8086 (mtp) cc_final: 0.7848 (mmp) REVERT: L 445 ASN cc_start: 0.8485 (m-40) cc_final: 0.8122 (m110) REVERT: L 492 GLU cc_start: 0.8664 (tp30) cc_final: 0.8387 (tt0) REVERT: L 501 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8309 (tm-30) REVERT: L 546 LEU cc_start: 0.9265 (mp) cc_final: 0.8929 (tt) REVERT: L 573 GLU cc_start: 0.8842 (tt0) cc_final: 0.8556 (mt-10) REVERT: L 619 ASP cc_start: 0.8225 (m-30) cc_final: 0.7942 (t0) REVERT: M 252 GLU cc_start: 0.8971 (tp30) cc_final: 0.8721 (pt0) REVERT: M 303 MET cc_start: 0.8457 (tpp) cc_final: 0.8153 (ttm) REVERT: M 308 GLU cc_start: 0.8614 (tt0) cc_final: 0.8389 (tp30) REVERT: M 501 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7797 (mp0) REVERT: M 506 ASN cc_start: 0.8377 (t0) cc_final: 0.7956 (p0) REVERT: M 533 GLN cc_start: 0.8515 (mt0) cc_final: 0.8246 (tt0) REVERT: M 573 GLU cc_start: 0.8986 (tt0) cc_final: 0.8662 (mt-10) REVERT: M 619 ASP cc_start: 0.7941 (m-30) cc_final: 0.7674 (t70) REVERT: N 412 MET cc_start: 0.8298 (mtp) cc_final: 0.8041 (mmp) REVERT: N 492 GLU cc_start: 0.8787 (tp30) cc_final: 0.8477 (tt0) REVERT: N 501 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8425 (tm-30) REVERT: N 609 TYR cc_start: 0.8686 (t80) cc_final: 0.8434 (t80) REVERT: N 619 ASP cc_start: 0.7989 (m-30) cc_final: 0.7716 (t70) REVERT: O 312 GLN cc_start: 0.8732 (mt0) cc_final: 0.8492 (mt0) REVERT: O 327 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8885 (p) REVERT: O 412 MET cc_start: 0.8094 (mtp) cc_final: 0.7844 (mmt) REVERT: O 492 GLU cc_start: 0.8678 (tp30) cc_final: 0.8348 (tt0) REVERT: O 573 GLU cc_start: 0.9015 (tp30) cc_final: 0.8667 (mt-10) REVERT: O 590 MET cc_start: 0.8077 (ttm) cc_final: 0.7827 (tmm) REVERT: O 595 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8476 (tp) REVERT: O 619 ASP cc_start: 0.8098 (m-30) cc_final: 0.7806 (t0) outliers start: 228 outliers final: 169 residues processed: 943 average time/residue: 0.4774 time to fit residues: 793.5099 Evaluate side-chains 871 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 694 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 132 HIS Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 415 VAL Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 420 THR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 531 ASP Chi-restraints excluded: chain H residue 533 GLN Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain H residue 635 HIS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 511 ASN Chi-restraints excluded: chain I residue 554 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 323 GLU Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 534 MET Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 235 MET Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 426 VAL Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 363 MET Chi-restraints excluded: chain L residue 415 VAL Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 537 LEU Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 363 MET Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 534 MET Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 415 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 522 GLN Chi-restraints excluded: chain O residue 549 GLU Chi-restraints excluded: chain O residue 595 ILE Chi-restraints excluded: chain O residue 603 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 0.6980 chunk 282 optimal weight: 4.9990 chunk 423 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 450 optimal weight: 9.9990 chunk 482 optimal weight: 6.9990 chunk 350 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 556 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5559 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= 0.295 Angle : 0.616 10.880 77175 Z= 0.311 Chirality : 0.046 0.283 9420 Planarity : 0.006 0.089 10065 Dihedral : 4.682 21.193 7875 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.89 % Favored : 91.91 % Rotamer: Outliers : 3.83 % Allowed : 19.53 % Favored : 76.63 % 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: -2.02 (0.10), residues: 7290 helix: 0.37 (0.11), residues: 2265 sheet: -2.25 (0.09), residues: 2625 loop : -1.62 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 419 HIS 0.004 0.001 HIS F 622 PHE 0.007 0.001 PHE D 642 TYR 0.026 0.002 TYR A 352 ARG 0.010 0.001 ARG H 181 *********************** 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 955 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 717 time to evaluate : 5.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8336 (tpp) cc_final: 0.8102 (tpp) REVERT: A 412 MET cc_start: 0.8064 (mtp) cc_final: 0.7838 (mmt) REVERT: A 445 ASN cc_start: 0.8485 (m-40) cc_final: 0.8125 (m110) REVERT: A 492 GLU cc_start: 0.8738 (tp30) cc_final: 0.8420 (tt0) REVERT: A 619 ASP cc_start: 0.8351 (m-30) cc_final: 0.8067 (t70) REVERT: A 620 ASP cc_start: 0.8577 (m-30) cc_final: 0.7779 (p0) REVERT: B 132 HIS cc_start: 0.2887 (OUTLIER) cc_final: 0.2607 (t70) REVERT: B 412 MET cc_start: 0.8097 (mmp) cc_final: 0.7499 (mtm) REVERT: B 492 GLU cc_start: 0.8815 (tp30) cc_final: 0.8526 (tt0) REVERT: B 619 ASP cc_start: 0.8063 (m-30) cc_final: 0.7820 (t0) REVERT: C 314 ASP cc_start: 0.8350 (t0) cc_final: 0.8057 (t0) REVERT: C 412 MET cc_start: 0.8211 (mtp) cc_final: 0.7969 (mmp) REVERT: C 492 GLU cc_start: 0.8841 (tp30) cc_final: 0.8531 (tt0) REVERT: C 501 GLU cc_start: 0.8570 (mp0) cc_final: 0.8200 (tm-30) REVERT: C 546 LEU cc_start: 0.9432 (mp) cc_final: 0.9064 (tp) REVERT: C 590 MET cc_start: 0.8234 (ttm) cc_final: 0.7948 (tmm) REVERT: C 619 ASP cc_start: 0.8453 (m-30) cc_final: 0.8199 (t70) REVERT: D 308 GLU cc_start: 0.8544 (tp30) cc_final: 0.8225 (mt-10) REVERT: D 312 GLN cc_start: 0.8873 (mt0) cc_final: 0.8602 (mt0) REVERT: D 327 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8834 (p) REVERT: D 412 MET cc_start: 0.8100 (mtp) cc_final: 0.7811 (mmp) REVERT: D 492 GLU cc_start: 0.8884 (tp30) cc_final: 0.8614 (tt0) REVERT: D 573 GLU cc_start: 0.8993 (tt0) cc_final: 0.8700 (mt-10) REVERT: D 619 ASP cc_start: 0.8466 (m-30) cc_final: 0.8140 (t70) REVERT: E 132 HIS cc_start: 0.3286 (OUTLIER) cc_final: 0.2837 (t70) REVERT: E 314 ASP cc_start: 0.8595 (t0) cc_final: 0.8272 (t0) REVERT: E 492 GLU cc_start: 0.8689 (tp30) cc_final: 0.8344 (tt0) REVERT: E 501 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8622 (tm-30) REVERT: E 506 ASN cc_start: 0.8549 (t0) cc_final: 0.8172 (p0) REVERT: E 606 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8575 (mm-30) REVERT: E 619 ASP cc_start: 0.8102 (m-30) cc_final: 0.7870 (t70) REVERT: F 454 GLU cc_start: 0.8733 (pt0) cc_final: 0.8500 (mt-10) REVERT: F 492 GLU cc_start: 0.8817 (tp30) cc_final: 0.8504 (tt0) REVERT: F 619 ASP cc_start: 0.8312 (m-30) cc_final: 0.8048 (t0) REVERT: G 412 MET cc_start: 0.8128 (mtp) cc_final: 0.7885 (mmp) REVERT: G 492 GLU cc_start: 0.8885 (tp30) cc_final: 0.8584 (tt0) REVERT: G 619 ASP cc_start: 0.8704 (m-30) cc_final: 0.8402 (t0) REVERT: H 412 MET cc_start: 0.7827 (mtp) cc_final: 0.7576 (mmp) REVERT: H 492 GLU cc_start: 0.8829 (tp30) cc_final: 0.8520 (tt0) REVERT: H 506 ASN cc_start: 0.8347 (t0) cc_final: 0.8146 (t0) REVERT: H 531 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8029 (t70) REVERT: H 573 GLU cc_start: 0.9092 (tp30) cc_final: 0.8811 (mt-10) REVERT: H 618 MET cc_start: 0.8276 (mtp) cc_final: 0.7951 (mtp) REVERT: H 619 ASP cc_start: 0.8668 (m-30) cc_final: 0.8442 (t70) REVERT: I 314 ASP cc_start: 0.8384 (t0) cc_final: 0.7858 (t0) REVERT: I 412 MET cc_start: 0.8057 (mtp) cc_final: 0.7805 (mmp) REVERT: I 492 GLU cc_start: 0.8808 (tp30) cc_final: 0.8497 (tt0) REVERT: I 501 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8534 (tm-30) REVERT: I 620 ASP cc_start: 0.8467 (m-30) cc_final: 0.7804 (p0) REVERT: I 634 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8471 (ttp-170) REVERT: I 635 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8051 (t-90) REVERT: J 312 GLN cc_start: 0.8681 (mt0) cc_final: 0.8378 (pt0) REVERT: J 412 MET cc_start: 0.8241 (mtp) cc_final: 0.7947 (mmp) REVERT: J 619 ASP cc_start: 0.8051 (m-30) cc_final: 0.7731 (t0) REVERT: J 634 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8518 (ttp-170) REVERT: K 235 MET cc_start: 0.4265 (OUTLIER) cc_final: 0.4064 (mmp) REVERT: K 314 ASP cc_start: 0.8451 (t0) cc_final: 0.8123 (t0) REVERT: K 412 MET cc_start: 0.8142 (mtp) cc_final: 0.7802 (mmp) REVERT: K 492 GLU cc_start: 0.8712 (tp30) cc_final: 0.8424 (tt0) REVERT: K 501 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8525 (tm-30) REVERT: K 573 GLU cc_start: 0.8888 (tt0) cc_final: 0.8578 (mt-10) REVERT: K 619 ASP cc_start: 0.7829 (m-30) cc_final: 0.7558 (t70) REVERT: L 303 MET cc_start: 0.8388 (tpp) cc_final: 0.8102 (tpp) REVERT: L 314 ASP cc_start: 0.8527 (t0) cc_final: 0.8172 (t0) REVERT: L 412 MET cc_start: 0.8072 (mtp) cc_final: 0.7748 (mmt) REVERT: L 445 ASN cc_start: 0.8547 (m-40) cc_final: 0.8194 (m110) REVERT: L 492 GLU cc_start: 0.8695 (tp30) cc_final: 0.8404 (tt0) REVERT: L 501 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8428 (tm-30) REVERT: L 546 LEU cc_start: 0.9270 (mp) cc_final: 0.8929 (tt) REVERT: L 573 GLU cc_start: 0.8861 (tt0) cc_final: 0.8574 (mt-10) REVERT: L 619 ASP cc_start: 0.8200 (m-30) cc_final: 0.7918 (t0) REVERT: M 252 GLU cc_start: 0.9023 (tp30) cc_final: 0.8763 (pt0) REVERT: M 303 MET cc_start: 0.8469 (tpp) cc_final: 0.8156 (ttm) REVERT: M 308 GLU cc_start: 0.8627 (tt0) cc_final: 0.8402 (tp30) REVERT: M 501 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7890 (mp0) REVERT: M 506 ASN cc_start: 0.8410 (t0) cc_final: 0.8172 (p0) REVERT: M 533 GLN cc_start: 0.8500 (mt0) cc_final: 0.8234 (tt0) REVERT: M 573 GLU cc_start: 0.8945 (tt0) cc_final: 0.8637 (mt-10) REVERT: M 619 ASP cc_start: 0.8008 (m-30) cc_final: 0.7749 (t70) REVERT: N 412 MET cc_start: 0.8316 (mtp) cc_final: 0.8036 (mmp) REVERT: N 492 GLU cc_start: 0.8790 (tp30) cc_final: 0.8479 (tt0) REVERT: N 501 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8442 (tm-30) REVERT: N 506 ASN cc_start: 0.8425 (t0) cc_final: 0.8054 (p0) REVERT: N 609 TYR cc_start: 0.8674 (t80) cc_final: 0.8298 (t80) REVERT: N 613 GLN cc_start: 0.7642 (mt0) cc_final: 0.7109 (pp30) REVERT: N 619 ASP cc_start: 0.8077 (m-30) cc_final: 0.7812 (t70) REVERT: O 327 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8858 (p) REVERT: O 412 MET cc_start: 0.8089 (mtp) cc_final: 0.7781 (mmp) REVERT: O 492 GLU cc_start: 0.8707 (tp30) cc_final: 0.8375 (tt0) REVERT: O 573 GLU cc_start: 0.9005 (tp30) cc_final: 0.8680 (mt-10) REVERT: O 590 MET cc_start: 0.8047 (ttm) cc_final: 0.7797 (tmm) REVERT: O 619 ASP cc_start: 0.8090 (m-30) cc_final: 0.7805 (t0) outliers start: 238 outliers final: 186 residues processed: 911 average time/residue: 0.4779 time to fit residues: 767.9429 Evaluate side-chains 885 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 692 time to evaluate : 4.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 635 HIS Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 635 HIS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 420 THR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 531 ASP Chi-restraints excluded: chain H residue 533 GLN Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain H residue 635 HIS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 554 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 ILE Chi-restraints excluded: chain I residue 635 HIS Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 323 GLU Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 534 MET Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 635 HIS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 235 MET Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 426 VAL Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 522 GLN Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 363 MET Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 522 GLN Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 537 LEU Chi-restraints excluded: chain L residue 554 LEU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 363 MET Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 534 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 534 MET Chi-restraints excluded: chain N residue 554 LEU Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 603 ILE Chi-restraints excluded: chain N residue 635 HIS Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 415 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 522 GLN Chi-restraints excluded: chain O residue 549 GLU Chi-restraints excluded: chain O residue 595 ILE Chi-restraints excluded: chain O residue 603 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 7.9990 chunk 678 optimal weight: 8.9990 chunk 619 optimal weight: 1.9990 chunk 660 optimal weight: 1.9990 chunk 397 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 518 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 596 optimal weight: 20.0000 chunk 624 optimal weight: 1.9990 chunk 657 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 489 GLN ** H 502 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** ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 57015 Z= 0.347 Angle : 0.640 8.279 77175 Z= 0.324 Chirality : 0.047 0.297 9420 Planarity : 0.006 0.087 10065 Dihedral : 4.796 22.871 7875 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.19 % Favored : 92.61 % Rotamer: Outliers : 3.82 % Allowed : 19.52 % Favored : 76.67 % 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: -2.09 (0.10), residues: 7290 helix: 0.33 (0.11), residues: 2280 sheet: -2.43 (0.09), residues: 2745 loop : -1.41 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 419 HIS 0.007 0.001 HIS J 622 PHE 0.009 0.002 PHE L 518 TYR 0.025 0.002 TYR E 352 ARG 0.009 0.001 ARG E 181 *********************** 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 946 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 709 time to evaluate : 4.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8378 (tpp) cc_final: 0.8148 (tpp) REVERT: A 314 ASP cc_start: 0.8706 (t0) cc_final: 0.8351 (t0) REVERT: A 412 MET cc_start: 0.8007 (mtp) cc_final: 0.7796 (mmt) REVERT: A 445 ASN cc_start: 0.8490 (m-40) cc_final: 0.8126 (m110) REVERT: A 492 GLU cc_start: 0.8768 (tp30) cc_final: 0.8440 (tt0) REVERT: A 619 ASP cc_start: 0.8359 (m-30) cc_final: 0.8076 (t70) REVERT: A 620 ASP cc_start: 0.8678 (m-30) cc_final: 0.7819 (p0) REVERT: B 132 HIS cc_start: 0.2864 (OUTLIER) cc_final: 0.2540 (t70) REVERT: B 308 GLU cc_start: 0.8593 (tp30) cc_final: 0.8385 (mt-10) REVERT: B 412 MET cc_start: 0.8053 (mmp) cc_final: 0.7452 (mtm) REVERT: B 492 GLU cc_start: 0.8868 (tp30) cc_final: 0.8586 (tt0) REVERT: B 619 ASP cc_start: 0.8230 (m-30) cc_final: 0.7979 (t0) REVERT: C 314 ASP cc_start: 0.8421 (t0) cc_final: 0.8164 (t0) REVERT: C 412 MET cc_start: 0.8114 (mtp) cc_final: 0.7883 (mmp) REVERT: C 492 GLU cc_start: 0.8848 (tp30) cc_final: 0.8538 (tt0) REVERT: C 501 GLU cc_start: 0.8572 (mp0) cc_final: 0.8224 (tm-30) REVERT: C 506 ASN cc_start: 0.8409 (t0) cc_final: 0.7692 (p0) REVERT: C 546 LEU cc_start: 0.9432 (mp) cc_final: 0.9132 (tt) REVERT: C 590 MET cc_start: 0.8249 (ttm) cc_final: 0.7959 (tmm) REVERT: C 619 ASP cc_start: 0.8547 (m-30) cc_final: 0.8297 (t70) REVERT: D 308 GLU cc_start: 0.8553 (tp30) cc_final: 0.8264 (mt-10) REVERT: D 312 GLN cc_start: 0.8899 (mt0) cc_final: 0.8640 (mt0) REVERT: D 327 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8830 (p) REVERT: D 412 MET cc_start: 0.8104 (mtp) cc_final: 0.7824 (mmp) REVERT: D 492 GLU cc_start: 0.8891 (tp30) cc_final: 0.8617 (tt0) REVERT: D 573 GLU cc_start: 0.8972 (tt0) cc_final: 0.8677 (mt-10) REVERT: D 619 ASP cc_start: 0.8492 (m-30) cc_final: 0.8164 (t70) REVERT: E 314 ASP cc_start: 0.8609 (t0) cc_final: 0.8269 (t0) REVERT: E 492 GLU cc_start: 0.8726 (tp30) cc_final: 0.8387 (tt0) REVERT: E 501 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8650 (tm-30) REVERT: E 506 ASN cc_start: 0.8599 (t0) cc_final: 0.8180 (p0) REVERT: E 606 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8585 (mm-30) REVERT: E 619 ASP cc_start: 0.8031 (m-30) cc_final: 0.7804 (t70) REVERT: F 173 ASN cc_start: 0.6299 (OUTLIER) cc_final: 0.6072 (m-40) REVERT: F 454 GLU cc_start: 0.8764 (pt0) cc_final: 0.8551 (mt-10) REVERT: F 492 GLU cc_start: 0.8850 (tp30) cc_final: 0.8552 (tt0) REVERT: F 619 ASP cc_start: 0.8324 (m-30) cc_final: 0.8070 (t0) REVERT: G 314 ASP cc_start: 0.8615 (t0) cc_final: 0.8326 (t0) REVERT: G 412 MET cc_start: 0.8043 (mtp) cc_final: 0.7783 (mmp) REVERT: G 414 LEU cc_start: 0.8257 (mm) cc_final: 0.7987 (pp) REVERT: G 492 GLU cc_start: 0.8866 (tp30) cc_final: 0.8556 (tt0) REVERT: G 531 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7977 (t70) REVERT: G 619 ASP cc_start: 0.8707 (m-30) cc_final: 0.8385 (t70) REVERT: H 314 ASP cc_start: 0.8556 (t0) cc_final: 0.8293 (t0) REVERT: H 412 MET cc_start: 0.7795 (mtp) cc_final: 0.7554 (mmp) REVERT: H 492 GLU cc_start: 0.8864 (tp30) cc_final: 0.8558 (tt0) REVERT: H 506 ASN cc_start: 0.8394 (t0) cc_final: 0.8186 (t0) REVERT: H 531 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8133 (t70) REVERT: H 618 MET cc_start: 0.8357 (mtp) cc_final: 0.8052 (mtp) REVERT: H 619 ASP cc_start: 0.8690 (m-30) cc_final: 0.8458 (t70) REVERT: I 314 ASP cc_start: 0.8451 (t0) cc_final: 0.7876 (t0) REVERT: I 412 MET cc_start: 0.8001 (mtp) cc_final: 0.7731 (mmp) REVERT: I 492 GLU cc_start: 0.8819 (tp30) cc_final: 0.8514 (tt0) REVERT: I 501 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8479 (tm-30) REVERT: I 634 ARG cc_start: 0.8855 (ttm-80) cc_final: 0.8492 (ttp-170) REVERT: I 635 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7995 (t-90) REVERT: J 179 MET cc_start: 0.7643 (tpt) cc_final: 0.7406 (tpp) REVERT: J 312 GLN cc_start: 0.8730 (mt0) cc_final: 0.8354 (pt0) REVERT: J 412 MET cc_start: 0.8223 (mtp) cc_final: 0.7906 (mmp) REVERT: J 618 MET cc_start: 0.8363 (ttp) cc_final: 0.7636 (ttp) REVERT: J 619 ASP cc_start: 0.7782 (m-30) cc_final: 0.7515 (t0) REVERT: J 634 ARG cc_start: 0.8899 (ttm-80) cc_final: 0.8521 (ttp-170) REVERT: K 235 MET cc_start: 0.4176 (OUTLIER) cc_final: 0.3587 (mmp) REVERT: K 314 ASP cc_start: 0.8467 (t0) cc_final: 0.8146 (t0) REVERT: K 412 MET cc_start: 0.8118 (mtp) cc_final: 0.7796 (mmp) REVERT: K 414 LEU cc_start: 0.8250 (mm) cc_final: 0.7949 (pp) REVERT: K 492 GLU cc_start: 0.8742 (tp30) cc_final: 0.8458 (tt0) REVERT: K 501 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8689 (tm-30) REVERT: K 573 GLU cc_start: 0.8883 (tt0) cc_final: 0.8566 (mt-10) REVERT: K 619 ASP cc_start: 0.7819 (m-30) cc_final: 0.7547 (t70) REVERT: L 303 MET cc_start: 0.8410 (tpp) cc_final: 0.8116 (tpp) REVERT: L 412 MET cc_start: 0.7952 (mtp) cc_final: 0.7659 (mmp) REVERT: L 445 ASN cc_start: 0.8552 (m-40) cc_final: 0.8178 (m110) REVERT: L 492 GLU cc_start: 0.8743 (tp30) cc_final: 0.8470 (tt0) REVERT: L 501 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8356 (tm-30) REVERT: L 546 LEU cc_start: 0.9274 (mp) cc_final: 0.8929 (tt) REVERT: L 573 GLU cc_start: 0.8840 (tt0) cc_final: 0.8563 (mt-10) REVERT: L 619 ASP cc_start: 0.8178 (m-30) cc_final: 0.7918 (t0) REVERT: L 620 ASP cc_start: 0.8603 (m-30) cc_final: 0.8042 (p0) REVERT: M 252 GLU cc_start: 0.8978 (tp30) cc_final: 0.8705 (pt0) REVERT: M 303 MET cc_start: 0.8477 (tpp) cc_final: 0.7902 (ttm) REVERT: M 307 GLN cc_start: 0.8510 (tp-100) cc_final: 0.7887 (mt0) REVERT: M 308 GLU cc_start: 0.8629 (tt0) cc_final: 0.8385 (tp30) REVERT: M 501 GLU cc_start: 0.8540 (tm-30) cc_final: 0.7869 (mp0) REVERT: M 533 GLN cc_start: 0.8454 (mt0) cc_final: 0.8189 (tt0) REVERT: M 573 GLU cc_start: 0.8946 (tt0) cc_final: 0.8630 (mt-10) REVERT: M 619 ASP cc_start: 0.8044 (m-30) cc_final: 0.7793 (t70) REVERT: M 638 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7395 (mm-30) REVERT: N 412 MET cc_start: 0.8364 (mtp) cc_final: 0.8090 (mmp) REVERT: N 492 GLU cc_start: 0.8810 (tp30) cc_final: 0.8501 (tt0) REVERT: N 501 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8455 (tm-30) REVERT: N 609 TYR cc_start: 0.8708 (t80) cc_final: 0.8339 (t80) REVERT: N 613 GLN cc_start: 0.7883 (mt0) cc_final: 0.7356 (pp30) REVERT: N 619 ASP cc_start: 0.7993 (m-30) cc_final: 0.7709 (t70) REVERT: O 314 ASP cc_start: 0.8714 (t0) cc_final: 0.8413 (t0) REVERT: O 327 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8842 (p) REVERT: O 412 MET cc_start: 0.8003 (mtp) cc_final: 0.7777 (mmt) REVERT: O 492 GLU cc_start: 0.8723 (tp30) cc_final: 0.8389 (tt0) REVERT: O 573 GLU cc_start: 0.9005 (tp30) cc_final: 0.8676 (mt-10) REVERT: O 590 MET cc_start: 0.8049 (ttm) cc_final: 0.7795 (tmm) REVERT: O 595 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8460 (tp) REVERT: O 619 ASP cc_start: 0.8132 (m-30) cc_final: 0.7838 (t0) outliers start: 237 outliers final: 197 residues processed: 900 average time/residue: 0.4750 time to fit residues: 752.7091 Evaluate side-chains 899 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 693 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 623 ILE Chi-restraints excluded: chain C residue 635 HIS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain F residue 173 ASN Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 531 ASP Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 420 THR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 531 ASP Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain H residue 635 HIS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 554 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 ILE Chi-restraints excluded: chain I residue 635 HIS Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 323 GLU Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 534 MET Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 623 ILE Chi-restraints excluded: chain J residue 635 HIS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 235 MET Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 426 VAL Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain K residue 449 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 522 GLN Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 363 MET Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 522 GLN Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 537 LEU Chi-restraints excluded: chain L residue 554 LEU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain L residue 623 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 363 MET Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 534 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 555 LEU Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 534 MET Chi-restraints excluded: chain N residue 554 LEU Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 603 ILE Chi-restraints excluded: chain N residue 635 HIS Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 415 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 522 GLN Chi-restraints excluded: chain O residue 549 GLU Chi-restraints excluded: chain O residue 595 ILE Chi-restraints excluded: chain O residue 603 ILE Chi-restraints excluded: chain O residue 635 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 8.9990 chunk 698 optimal weight: 6.9990 chunk 426 optimal weight: 0.9980 chunk 331 optimal weight: 0.7980 chunk 485 optimal weight: 4.9990 chunk 732 optimal weight: 0.2980 chunk 673 optimal weight: 0.7980 chunk 583 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 450 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 408 ASN ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** G 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 GLN ** H 502 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 266 GLN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 445 ASN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 576 ASN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5933 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= 0.194 Angle : 0.581 12.121 77175 Z= 0.295 Chirality : 0.046 0.212 9420 Planarity : 0.005 0.085 10065 Dihedral : 4.435 20.177 7875 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.88 % Favored : 94.91 % Rotamer: Outliers : 2.53 % Allowed : 20.90 % Favored : 76.57 % 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: -1.85 (0.10), residues: 7290 helix: 0.53 (0.11), residues: 2280 sheet: -2.43 (0.09), residues: 2730 loop : -1.10 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 341 HIS 0.003 0.000 HIS I 635 PHE 0.007 0.001 PHE D 450 TYR 0.019 0.001 TYR O 609 ARG 0.013 0.000 ARG B 181 ********************** 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 913 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 756 time to evaluate : 4.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8276 (tpp) cc_final: 0.8023 (tpp) REVERT: A 412 MET cc_start: 0.8043 (mtp) cc_final: 0.7825 (mmt) REVERT: A 445 ASN cc_start: 0.8281 (m-40) cc_final: 0.7924 (m110) REVERT: A 492 GLU cc_start: 0.8668 (tp30) cc_final: 0.8348 (tt0) REVERT: A 619 ASP cc_start: 0.8152 (m-30) cc_final: 0.7845 (t70) REVERT: A 620 ASP cc_start: 0.8461 (m-30) cc_final: 0.7667 (p0) REVERT: B 132 HIS cc_start: 0.2971 (OUTLIER) cc_final: 0.2612 (t70) REVERT: B 303 MET cc_start: 0.8002 (mmm) cc_final: 0.7470 (ttm) REVERT: B 412 MET cc_start: 0.8051 (mmp) cc_final: 0.7428 (mtm) REVERT: B 492 GLU cc_start: 0.8736 (tp30) cc_final: 0.8421 (tt0) REVERT: B 619 ASP cc_start: 0.8028 (m-30) cc_final: 0.7729 (t70) REVERT: C 412 MET cc_start: 0.8184 (mtp) cc_final: 0.7844 (mmp) REVERT: C 492 GLU cc_start: 0.8799 (tp30) cc_final: 0.8490 (tt0) REVERT: C 501 GLU cc_start: 0.8274 (mp0) cc_final: 0.8000 (tm-30) REVERT: C 506 ASN cc_start: 0.8274 (t0) cc_final: 0.7858 (p0) REVERT: C 546 LEU cc_start: 0.9445 (mp) cc_final: 0.9137 (tt) REVERT: C 619 ASP cc_start: 0.8551 (m-30) cc_final: 0.8302 (t70) REVERT: D 308 GLU cc_start: 0.8415 (tp30) cc_final: 0.8137 (mt-10) REVERT: D 312 GLN cc_start: 0.8887 (mt0) cc_final: 0.8663 (mt0) REVERT: D 314 ASP cc_start: 0.8522 (t0) cc_final: 0.8304 (p0) REVERT: D 327 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8879 (p) REVERT: D 412 MET cc_start: 0.8114 (mtp) cc_final: 0.7812 (mmp) REVERT: D 492 GLU cc_start: 0.8765 (tp30) cc_final: 0.8490 (tt0) REVERT: D 573 GLU cc_start: 0.8975 (tt0) cc_final: 0.8677 (mt-10) REVERT: D 619 ASP cc_start: 0.8423 (m-30) cc_final: 0.8075 (t70) REVERT: D 620 ASP cc_start: 0.8411 (m-30) cc_final: 0.7637 (p0) REVERT: E 132 HIS cc_start: 0.3020 (OUTLIER) cc_final: 0.2688 (t70) REVERT: E 314 ASP cc_start: 0.8288 (t0) cc_final: 0.7995 (t0) REVERT: E 492 GLU cc_start: 0.8625 (tp30) cc_final: 0.8274 (tt0) REVERT: E 501 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8444 (tm-30) REVERT: E 506 ASN cc_start: 0.8499 (t0) cc_final: 0.8177 (p0) REVERT: E 619 ASP cc_start: 0.7852 (m-30) cc_final: 0.7623 (t70) REVERT: F 312 GLN cc_start: 0.8780 (mt0) cc_final: 0.8551 (pt0) REVERT: F 492 GLU cc_start: 0.8760 (tp30) cc_final: 0.8448 (tt0) REVERT: F 619 ASP cc_start: 0.8088 (m-30) cc_final: 0.7788 (t0) REVERT: G 314 ASP cc_start: 0.8352 (t0) cc_final: 0.8087 (p0) REVERT: G 412 MET cc_start: 0.8202 (mtp) cc_final: 0.7868 (mmp) REVERT: G 414 LEU cc_start: 0.8163 (mm) cc_final: 0.7921 (pp) REVERT: G 492 GLU cc_start: 0.8692 (tp30) cc_final: 0.8324 (tt0) REVERT: G 619 ASP cc_start: 0.8681 (m-30) cc_final: 0.8382 (t0) REVERT: H 412 MET cc_start: 0.7909 (mtp) cc_final: 0.7624 (mmp) REVERT: H 492 GLU cc_start: 0.8658 (tp30) cc_final: 0.8341 (tt0) REVERT: H 573 GLU cc_start: 0.9126 (tp30) cc_final: 0.8851 (mt-10) REVERT: H 618 MET cc_start: 0.8169 (mtp) cc_final: 0.7808 (mtp) REVERT: H 619 ASP cc_start: 0.8529 (m-30) cc_final: 0.8265 (t70) REVERT: I 246 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8303 (mt) REVERT: I 412 MET cc_start: 0.8160 (mtp) cc_final: 0.7897 (mmp) REVERT: I 492 GLU cc_start: 0.8681 (tp30) cc_final: 0.8372 (tt0) REVERT: I 501 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8258 (tm-30) REVERT: I 634 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8388 (ttp-170) REVERT: I 635 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7881 (t-90) REVERT: J 179 MET cc_start: 0.7616 (tpt) cc_final: 0.7374 (tpp) REVERT: J 312 GLN cc_start: 0.8707 (mt0) cc_final: 0.8402 (pt0) REVERT: J 412 MET cc_start: 0.8309 (mtp) cc_final: 0.7971 (mmp) REVERT: J 618 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7822 (ttt) REVERT: J 634 ARG cc_start: 0.8871 (ttm-80) cc_final: 0.8501 (ttp-170) REVERT: K 157 ARG cc_start: 0.3506 (mmt180) cc_final: 0.3279 (mmt90) REVERT: K 303 MET cc_start: 0.7872 (mmm) cc_final: 0.7125 (mtm) REVERT: K 314 ASP cc_start: 0.8248 (t0) cc_final: 0.7960 (t0) REVERT: K 412 MET cc_start: 0.8214 (mtp) cc_final: 0.7870 (mmp) REVERT: K 414 LEU cc_start: 0.8254 (mm) cc_final: 0.7982 (pp) REVERT: K 492 GLU cc_start: 0.8662 (tp30) cc_final: 0.8381 (tt0) REVERT: K 501 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8467 (tm-30) REVERT: K 573 GLU cc_start: 0.8932 (tt0) cc_final: 0.8643 (mt-10) REVERT: K 619 ASP cc_start: 0.7804 (m-30) cc_final: 0.7596 (t70) REVERT: L 303 MET cc_start: 0.8360 (tpp) cc_final: 0.8099 (tpp) REVERT: L 412 MET cc_start: 0.7973 (mtp) cc_final: 0.7713 (mmp) REVERT: L 492 GLU cc_start: 0.8640 (tp30) cc_final: 0.8339 (tt0) REVERT: L 501 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8060 (tm-30) REVERT: L 546 LEU cc_start: 0.9284 (mp) cc_final: 0.8915 (tt) REVERT: L 573 GLU cc_start: 0.8853 (tt0) cc_final: 0.8563 (mt-10) REVERT: L 619 ASP cc_start: 0.8132 (m-30) cc_final: 0.7852 (t70) REVERT: M 252 GLU cc_start: 0.8821 (tp30) cc_final: 0.8593 (pt0) REVERT: M 303 MET cc_start: 0.8375 (tpp) cc_final: 0.8110 (tpp) REVERT: M 308 GLU cc_start: 0.8550 (tt0) cc_final: 0.8297 (tp30) REVERT: M 506 ASN cc_start: 0.8360 (t0) cc_final: 0.8007 (p0) REVERT: M 533 GLN cc_start: 0.8496 (mt0) cc_final: 0.8248 (tt0) REVERT: M 573 GLU cc_start: 0.8964 (tt0) cc_final: 0.8648 (mt-10) REVERT: M 619 ASP cc_start: 0.7960 (m-30) cc_final: 0.7718 (t70) REVERT: N 412 MET cc_start: 0.8434 (mtp) cc_final: 0.8133 (mmp) REVERT: N 414 LEU cc_start: 0.8069 (mm) cc_final: 0.7834 (pp) REVERT: N 492 GLU cc_start: 0.8664 (tp30) cc_final: 0.8343 (tt0) REVERT: N 501 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8229 (tm-30) REVERT: N 506 ASN cc_start: 0.8378 (t0) cc_final: 0.7998 (p0) REVERT: N 609 TYR cc_start: 0.8564 (t80) cc_final: 0.8282 (t80) REVERT: N 619 ASP cc_start: 0.7844 (m-30) cc_final: 0.7546 (t70) REVERT: O 412 MET cc_start: 0.8136 (mtp) cc_final: 0.7837 (mmp) REVERT: O 492 GLU cc_start: 0.8619 (tp30) cc_final: 0.8286 (tt0) REVERT: O 573 GLU cc_start: 0.9007 (tp30) cc_final: 0.8674 (mt-10) REVERT: O 590 MET cc_start: 0.8056 (ttm) cc_final: 0.7837 (tmm) REVERT: O 595 ILE cc_start: 0.8702 (mt) cc_final: 0.8422 (tp) REVERT: O 619 ASP cc_start: 0.7960 (m-30) cc_final: 0.7650 (t70) outliers start: 157 outliers final: 119 residues processed: 886 average time/residue: 0.4970 time to fit residues: 767.8154 Evaluate side-chains 796 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 671 time to evaluate : 4.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 420 THR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 554 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 ILE Chi-restraints excluded: chain I residue 635 HIS Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 618 MET Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 363 MET Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 522 GLN Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 537 LEU Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain L residue 623 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 363 MET Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 554 LEU Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 603 ILE Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 522 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 2.9990 chunk 621 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 537 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 584 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 599 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 107 optimal weight: 0.0270 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN B 312 GLN B 489 GLN C 266 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 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 489 GLN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 576 ASN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.194967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156996 restraints weight = 72145.354| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.64 r_work: 0.3749 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 57015 Z= 0.189 Angle : 0.568 9.767 77175 Z= 0.289 Chirality : 0.046 0.199 9420 Planarity : 0.005 0.083 10065 Dihedral : 4.290 20.518 7875 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.27 % Favored : 94.53 % Rotamer: Outliers : 2.17 % Allowed : 21.35 % Favored : 76.47 % 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: 0.65 (0.11), residues: 2280 sheet: -2.25 (0.10), residues: 2610 loop : -1.17 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 419 HIS 0.003 0.001 HIS I 635 PHE 0.006 0.001 PHE J 565 TYR 0.022 0.001 TYR O 609 ARG 0.012 0.000 ARG B 181 =============================================================================== Job complete usr+sys time: 14164.04 seconds wall clock time: 249 minutes 21.86 seconds (14961.86 seconds total)