Starting phenix.real_space_refine on Wed Sep 25 12:08:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/09_2024/6i1y_0327_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/09_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_0327/09_2024/6i1y_0327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/09_2024/6i1y_0327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/09_2024/6i1y_0327_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/09_2024/6i1y_0327_neut.cif" } 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. Time to flip 39 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 56520 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "B" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "C" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "D" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "E" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "F" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "G" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "H" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "I" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "J" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "K" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "L" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "M" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "N" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "O" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Time building chain proxies: 22.54, per 1000 atoms: 0.40 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 - 3.00 Amino acid : True - 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: 10.83 Conformation dependent library (CDL) restraints added in 5.6 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: 3.28 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: 14.17 Time building geometry restraints manager: 12.98 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: 0.00 - 2.76: 65433 2.76 - 5.52: 10926 5.52 - 8.28: 681 8.28 - 11.04: 60 11.04 - 13.80: 75 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 3.040 nonbonded pdb=" O GLN K 312 " pdb=" OH TYR L 245 " model vdw 1.302 3.040 nonbonded pdb=" O GLN D 312 " pdb=" OH TYR E 245 " model vdw 1.304 3.040 nonbonded pdb=" OH TYR A 245 " pdb=" O GLN O 312 " model vdw 1.306 3.040 nonbonded pdb=" O GLN A 312 " pdb=" OH TYR B 245 " model vdw 1.307 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.040 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: 1.530 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 87.320 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.410 ------------------------------------------------------------------------------- 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 : 4.725 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: 0.5600 time to fit residues: 1282.1228 Evaluate side-chains 875 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 853 time to evaluate : 4.706 ------------------------------------------------------------------------------- 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: 1.9990 chunk 309 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 375 optimal weight: 0.6980 chunk 297 optimal weight: 20.0000 chunk 576 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 chunk 428 optimal weight: 0.9990 chunk 667 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 241 ASN B 264 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN C 264 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN D 264 ASN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 241 ASN E 264 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS F 241 ASN F 264 ASN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 241 ASN G 264 ASN 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 ** 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 J 288 HIS J 408 ASN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 524 ASN K 241 ASN K 264 ASN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 HIS L 264 ASN L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 132 HIS M 241 ASN M 264 ASN ** M 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 524 ASN N 241 ASN N 264 ASN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 241 ASN O 264 ASN ** O 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3627 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= 0.290 Angle : 0.740 8.617 77175 Z= 0.385 Chirality : 0.050 0.212 9420 Planarity : 0.007 0.104 10065 Dihedral : 6.366 47.284 7942 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.46 % Favored : 93.33 % Rotamer: Outliers : 1.80 % Allowed : 11.30 % Favored : 86.89 % 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: -3.52 (0.09), residues: 7290 helix: -1.39 (0.10), residues: 2280 sheet: -2.79 (0.09), residues: 2580 loop : -2.33 (0.11), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 419 HIS 0.007 0.001 HIS C 132 PHE 0.016 0.002 PHE G 642 TYR 0.020 0.003 TYR D 133 ARG 0.008 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 1294 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1182 time to evaluate : 4.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.7899 (tpp) cc_final: 0.7426 (ttm) REVERT: A 314 ASP cc_start: 0.8364 (t0) cc_final: 0.8089 (t0) REVERT: A 412 MET cc_start: 0.8261 (mtp) cc_final: 0.7819 (mmp) REVERT: A 492 GLU cc_start: 0.8747 (tp30) cc_final: 0.8339 (tt0) REVERT: A 501 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8214 (tm-30) REVERT: A 520 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8792 (ptmm) REVERT: A 590 MET cc_start: 0.8372 (ttm) cc_final: 0.8113 (tmm) REVERT: A 619 ASP cc_start: 0.8637 (m-30) cc_final: 0.8374 (t70) REVERT: A 633 LYS cc_start: 0.7083 (tppt) cc_final: 0.6831 (tptt) REVERT: B 303 MET cc_start: 0.8152 (tpp) cc_final: 0.7783 (ttm) REVERT: B 412 MET cc_start: 0.8292 (mtp) cc_final: 0.8032 (mmt) REVERT: B 445 ASN cc_start: 0.8345 (m-40) cc_final: 0.8119 (m110) REVERT: B 492 GLU cc_start: 0.8779 (tp30) cc_final: 0.8459 (tt0) REVERT: B 501 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8488 (tm-30) REVERT: B 588 ASP cc_start: 0.8358 (m-30) cc_final: 0.8153 (p0) REVERT: B 619 ASP cc_start: 0.8493 (m-30) cc_final: 0.8226 (t0) REVERT: C 412 MET cc_start: 0.8286 (mtp) cc_final: 0.7722 (mmp) REVERT: C 492 GLU cc_start: 0.8714 (tp30) cc_final: 0.8252 (tt0) REVERT: C 533 GLN cc_start: 0.8682 (mt0) cc_final: 0.8440 (tt0) REVERT: C 590 MET cc_start: 0.8212 (ttm) cc_final: 0.7899 (tmm) REVERT: C 619 ASP cc_start: 0.8615 (m-30) cc_final: 0.8374 (t70) REVERT: D 314 ASP cc_start: 0.8471 (t0) cc_final: 0.8242 (t0) REVERT: D 412 MET cc_start: 0.8304 (mtp) cc_final: 0.7966 (mmp) REVERT: D 445 ASN cc_start: 0.8379 (m-40) cc_final: 0.8092 (m110) REVERT: D 492 GLU cc_start: 0.8759 (tp30) cc_final: 0.8389 (tt0) REVERT: D 501 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8141 (tm-30) REVERT: D 522 GLN cc_start: 0.9016 (tt0) cc_final: 0.8709 (tt0) REVERT: D 533 GLN cc_start: 0.8553 (mt0) cc_final: 0.8352 (tt0) REVERT: D 573 GLU cc_start: 0.9043 (tt0) cc_final: 0.8795 (mt-10) REVERT: D 595 ILE cc_start: 0.9034 (mt) cc_final: 0.8831 (tp) REVERT: D 619 ASP cc_start: 0.8388 (m-30) cc_final: 0.8098 (t0) REVERT: E 308 GLU cc_start: 0.8705 (tt0) cc_final: 0.8436 (tp30) REVERT: E 314 ASP cc_start: 0.8488 (t0) cc_final: 0.8185 (t0) REVERT: E 492 GLU cc_start: 0.8482 (tp30) cc_final: 0.8156 (tt0) REVERT: E 501 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8315 (tm-30) REVERT: E 534 MET cc_start: 0.9025 (ttp) cc_final: 0.8721 (ttp) REVERT: E 619 ASP cc_start: 0.8535 (m-30) cc_final: 0.8156 (t70) REVERT: F 297 THR cc_start: 0.9118 (m) cc_final: 0.8446 (m) REVERT: F 303 MET cc_start: 0.8287 (tpp) cc_final: 0.7981 (ttm) REVERT: F 314 ASP cc_start: 0.8358 (t0) cc_final: 0.8085 (t0) REVERT: F 412 MET cc_start: 0.8244 (mtp) cc_final: 0.7972 (mmp) REVERT: F 492 GLU cc_start: 0.8782 (tp30) cc_final: 0.8433 (tt0) REVERT: F 522 GLN cc_start: 0.8988 (tt0) cc_final: 0.8763 (tt0) REVERT: F 590 MET cc_start: 0.8429 (ttm) cc_final: 0.8170 (tmm) REVERT: F 619 ASP cc_start: 0.8537 (m-30) cc_final: 0.8264 (t0) REVERT: G 297 THR cc_start: 0.9106 (m) cc_final: 0.8275 (m) REVERT: G 312 GLN cc_start: 0.8948 (mt0) cc_final: 0.8663 (mt0) REVERT: G 314 ASP cc_start: 0.8398 (t0) cc_final: 0.8003 (t0) REVERT: G 412 MET cc_start: 0.8336 (mtp) cc_final: 0.7945 (mmp) REVERT: G 492 GLU cc_start: 0.8856 (tp30) cc_final: 0.8465 (tt0) REVERT: G 506 ASN cc_start: 0.8255 (t0) cc_final: 0.8049 (t0) REVERT: G 522 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: G 619 ASP cc_start: 0.8741 (m-30) cc_final: 0.8456 (t0) REVERT: H 241 ASN cc_start: 0.8296 (p0) cc_final: 0.8060 (m110) REVERT: H 412 MET cc_start: 0.8152 (mtp) cc_final: 0.7641 (mmp) REVERT: H 492 GLU cc_start: 0.8757 (tp30) cc_final: 0.8354 (tt0) REVERT: H 506 ASN cc_start: 0.8295 (t0) cc_final: 0.8057 (t0) REVERT: H 533 GLN cc_start: 0.8615 (mt0) cc_final: 0.8364 (tt0) REVERT: H 573 GLU cc_start: 0.8954 (tt0) cc_final: 0.8702 (mt-10) REVERT: H 618 MET cc_start: 0.8218 (mtp) cc_final: 0.7978 (mtp) REVERT: H 619 ASP cc_start: 0.8729 (m-30) cc_final: 0.8476 (t70) REVERT: I 303 MET cc_start: 0.8316 (tpp) cc_final: 0.7935 (ttm) REVERT: I 308 GLU cc_start: 0.8709 (tp30) cc_final: 0.8469 (tp30) REVERT: I 314 ASP cc_start: 0.8518 (t0) cc_final: 0.8121 (t0) REVERT: I 341 TRP cc_start: 0.9052 (m100) cc_final: 0.8839 (m100) REVERT: I 412 MET cc_start: 0.8178 (mtp) cc_final: 0.7779 (mmp) REVERT: I 492 GLU cc_start: 0.8615 (tp30) cc_final: 0.8289 (tt0) REVERT: I 501 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8250 (tm-30) REVERT: I 533 GLN cc_start: 0.8539 (mt0) cc_final: 0.8332 (tt0) REVERT: I 619 ASP cc_start: 0.8543 (m-30) cc_final: 0.8265 (t70) REVERT: J 303 MET cc_start: 0.8251 (tpp) cc_final: 0.7958 (ttm) REVERT: J 314 ASP cc_start: 0.8264 (t0) cc_final: 0.7961 (t0) REVERT: J 412 MET cc_start: 0.8284 (mtp) cc_final: 0.7893 (mmp) REVERT: J 445 ASN cc_start: 0.8451 (m-40) cc_final: 0.8185 (m110) REVERT: J 492 GLU cc_start: 0.8642 (tp30) cc_final: 0.8427 (tt0) REVERT: J 501 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8361 (tm-30) REVERT: J 522 GLN cc_start: 0.9069 (tt0) cc_final: 0.8846 (tt0) REVERT: J 619 ASP cc_start: 0.8631 (m-30) cc_final: 0.8395 (t0) REVERT: K 303 MET cc_start: 0.8167 (tpp) cc_final: 0.7929 (tpp) REVERT: K 308 GLU cc_start: 0.8814 (tt0) cc_final: 0.8613 (tp30) REVERT: K 314 ASP cc_start: 0.8451 (t0) cc_final: 0.7869 (t0) REVERT: K 412 MET cc_start: 0.8106 (mtp) cc_final: 0.7749 (mmp) REVERT: K 492 GLU cc_start: 0.8645 (tp30) cc_final: 0.8305 (tt0) REVERT: K 501 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8211 (tm-30) REVERT: K 533 GLN cc_start: 0.8776 (mt0) cc_final: 0.8567 (tt0) REVERT: K 573 GLU cc_start: 0.8884 (tt0) cc_final: 0.8613 (mt-10) REVERT: K 619 ASP cc_start: 0.8500 (m-30) cc_final: 0.8224 (t70) REVERT: L 303 MET cc_start: 0.8366 (tpp) cc_final: 0.8063 (tpp) REVERT: L 412 MET cc_start: 0.8173 (mtp) cc_final: 0.7772 (mmt) REVERT: L 492 GLU cc_start: 0.8694 (tp30) cc_final: 0.8362 (tt0) REVERT: L 501 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8142 (tm-30) REVERT: L 573 GLU cc_start: 0.8951 (tt0) cc_final: 0.8671 (mt-10) REVERT: L 619 ASP cc_start: 0.8603 (m-30) cc_final: 0.8360 (t0) REVERT: M 252 GLU cc_start: 0.9065 (tp30) cc_final: 0.8835 (pt0) REVERT: M 303 MET cc_start: 0.8384 (tpp) cc_final: 0.8039 (ttm) REVERT: M 308 GLU cc_start: 0.8614 (tt0) cc_final: 0.8411 (tp30) REVERT: M 314 ASP cc_start: 0.8523 (t0) cc_final: 0.8116 (t0) REVERT: M 412 MET cc_start: 0.8299 (mtp) cc_final: 0.7894 (mmp) REVERT: M 445 ASN cc_start: 0.8529 (m110) cc_final: 0.8297 (m110) REVERT: M 501 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8221 (tm-30) REVERT: M 524 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8181 (p0) REVERT: M 533 GLN cc_start: 0.8611 (mt0) cc_final: 0.8302 (tt0) REVERT: M 573 GLU cc_start: 0.9062 (tt0) cc_final: 0.8780 (mt-10) REVERT: M 595 ILE cc_start: 0.9046 (mt) cc_final: 0.8759 (tp) REVERT: M 609 TYR cc_start: 0.8762 (t80) cc_final: 0.8528 (t80) REVERT: M 619 ASP cc_start: 0.8502 (m-30) cc_final: 0.8222 (t0) REVERT: N 297 THR cc_start: 0.9064 (m) cc_final: 0.8238 (m) REVERT: N 312 GLN cc_start: 0.8750 (mt0) cc_final: 0.8385 (mt0) REVERT: N 412 MET cc_start: 0.8312 (mtp) cc_final: 0.8002 (mmp) REVERT: N 444 ASP cc_start: 0.8291 (m-30) cc_final: 0.7809 (t0) REVERT: N 492 GLU cc_start: 0.8732 (tp30) cc_final: 0.8403 (tt0) REVERT: N 501 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8201 (tm-30) REVERT: N 533 GLN cc_start: 0.8686 (mt0) cc_final: 0.8486 (tt0) REVERT: N 619 ASP cc_start: 0.8534 (m-30) cc_final: 0.8257 (t0) REVERT: O 297 THR cc_start: 0.9171 (m) cc_final: 0.8422 (m) REVERT: O 308 GLU cc_start: 0.8699 (tt0) cc_final: 0.8377 (tp30) REVERT: O 312 GLN cc_start: 0.8703 (mt0) cc_final: 0.8327 (mt0) REVERT: O 314 ASP cc_start: 0.8488 (t0) cc_final: 0.8149 (t0) REVERT: O 412 MET cc_start: 0.8258 (mtp) cc_final: 0.7840 (mmp) REVERT: O 445 ASN cc_start: 0.8597 (m110) cc_final: 0.8366 (m-40) REVERT: O 492 GLU cc_start: 0.8624 (tp30) cc_final: 0.8219 (tt0) REVERT: O 506 ASN cc_start: 0.8351 (t0) cc_final: 0.8149 (t0) REVERT: O 573 GLU cc_start: 0.8858 (tt0) cc_final: 0.8588 (mt-10) REVERT: O 595 ILE cc_start: 0.8963 (mt) cc_final: 0.8712 (tp) REVERT: O 619 ASP cc_start: 0.8686 (m-30) cc_final: 0.8419 (t0) outliers start: 112 outliers final: 29 residues processed: 1249 average time/residue: 0.5391 time to fit residues: 1178.5302 Evaluate side-chains 919 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 888 time to evaluate : 4.771 ------------------------------------------------------------------------------- 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 B residue 241 ASN Chi-restraints excluded: chain B residue 526 SER 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 246 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain G residue 520 LYS Chi-restraints excluded: chain G residue 522 GLN 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 370 LYS 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 L residue 363 MET Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 524 ASN Chi-restraints excluded: chain N residue 323 GLU Chi-restraints excluded: chain O residue 186 LEU 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: 0.9980 chunk 207 optimal weight: 2.9990 chunk 555 optimal weight: 8.9990 chunk 454 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 668 optimal weight: 1.9990 chunk 722 optimal weight: 4.9990 chunk 595 optimal weight: 20.0000 chunk 663 optimal weight: 8.9990 chunk 227 optimal weight: 0.8980 chunk 536 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 288 HIS B 502 GLN C 241 ASN C 288 HIS ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 HIS E 288 HIS ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 511 ASN ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN H 241 ASN H 288 HIS H 408 ASN ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 601 ASN I 288 HIS I 445 ASN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 ASN J 289 GLN J 524 ASN K 241 ASN K 288 HIS ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 HIS L 445 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 288 HIS M 312 GLN M 445 ASN ** N 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 HIS O 288 HIS ** O 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 57015 Z= 0.251 Angle : 0.648 7.684 77175 Z= 0.329 Chirality : 0.047 0.221 9420 Planarity : 0.006 0.102 10065 Dihedral : 5.265 54.506 7878 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.50 % Favored : 94.29 % Rotamer: Outliers : 2.91 % Allowed : 14.06 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.09), residues: 7290 helix: -0.37 (0.10), residues: 2295 sheet: -2.67 (0.09), residues: 2475 loop : -2.09 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 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 1121 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 940 time to evaluate : 4.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8008 (tpp) cc_final: 0.7655 (ttm) REVERT: A 314 ASP cc_start: 0.8498 (t0) cc_final: 0.8100 (t0) REVERT: A 412 MET cc_start: 0.8169 (mtp) cc_final: 0.7708 (mmp) REVERT: A 445 ASN cc_start: 0.8512 (m-40) cc_final: 0.8133 (m110) REVERT: A 492 GLU cc_start: 0.8696 (tp30) cc_final: 0.8364 (tt0) REVERT: A 501 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8391 (mp0) REVERT: A 619 ASP cc_start: 0.8593 (m-30) cc_final: 0.8355 (t70) REVERT: A 620 ASP cc_start: 0.8489 (m-30) cc_final: 0.7747 (p0) REVERT: A 633 LYS cc_start: 0.7152 (tppt) cc_final: 0.6883 (tptt) REVERT: B 265 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7260 (tt) REVERT: B 303 MET cc_start: 0.8160 (tpp) cc_final: 0.7893 (tpp) REVERT: B 412 MET cc_start: 0.8141 (mtp) cc_final: 0.7832 (mmt) REVERT: B 444 ASP cc_start: 0.7915 (m-30) cc_final: 0.7611 (t0) REVERT: B 492 GLU cc_start: 0.8852 (tp30) cc_final: 0.8576 (tt0) REVERT: B 501 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8505 (tm-30) REVERT: B 506 ASN cc_start: 0.8432 (t0) cc_final: 0.7751 (p0) REVERT: B 619 ASP cc_start: 0.8433 (m-30) cc_final: 0.8209 (t0) REVERT: C 308 GLU cc_start: 0.8711 (tp30) cc_final: 0.8456 (mt-10) REVERT: C 314 ASP cc_start: 0.8230 (t0) cc_final: 0.7880 (t0) REVERT: C 412 MET cc_start: 0.8187 (mtp) cc_final: 0.7824 (mmp) REVERT: C 492 GLU cc_start: 0.8811 (tp30) cc_final: 0.8514 (tt0) REVERT: C 590 MET cc_start: 0.8257 (ttm) cc_final: 0.7957 (tmm) REVERT: C 619 ASP cc_start: 0.8590 (m-30) cc_final: 0.8375 (t70) REVERT: D 308 GLU cc_start: 0.8779 (tp30) cc_final: 0.8514 (tp30) REVERT: D 312 GLN cc_start: 0.9033 (mt0) cc_final: 0.8789 (mt0) REVERT: D 327 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8786 (p) REVERT: D 412 MET cc_start: 0.8139 (mtp) cc_final: 0.7856 (mmp) REVERT: D 445 ASN cc_start: 0.8497 (m-40) cc_final: 0.8263 (m110) REVERT: D 492 GLU cc_start: 0.8748 (tp30) cc_final: 0.8439 (tt0) REVERT: D 501 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8119 (tm-30) REVERT: D 520 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8713 (ptmm) REVERT: D 522 GLN cc_start: 0.8992 (tt0) cc_final: 0.8615 (tt0) REVERT: D 573 GLU cc_start: 0.9021 (tt0) cc_final: 0.8767 (mt-10) REVERT: D 595 ILE cc_start: 0.8820 (mt) cc_final: 0.8576 (tp) REVERT: D 619 ASP cc_start: 0.8383 (m-30) cc_final: 0.8068 (t0) REVERT: E 308 GLU cc_start: 0.8815 (tt0) cc_final: 0.8604 (tp30) REVERT: E 314 ASP cc_start: 0.8588 (t0) cc_final: 0.8196 (t0) REVERT: E 492 GLU cc_start: 0.8567 (tp30) cc_final: 0.8232 (tt0) REVERT: E 501 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8353 (tm-30) REVERT: E 619 ASP cc_start: 0.8165 (m-30) cc_final: 0.7919 (t70) REVERT: F 303 MET cc_start: 0.8263 (tpp) cc_final: 0.8004 (ttm) REVERT: F 314 ASP cc_start: 0.8262 (t0) cc_final: 0.8012 (t0) REVERT: F 412 MET cc_start: 0.8185 (mtp) cc_final: 0.7871 (mmp) REVERT: F 445 ASN cc_start: 0.8764 (m-40) cc_final: 0.8342 (m110) REVERT: F 492 GLU cc_start: 0.8785 (tp30) cc_final: 0.8487 (tt0) REVERT: F 506 ASN cc_start: 0.8408 (t0) cc_final: 0.7766 (p0) REVERT: F 522 GLN cc_start: 0.8979 (tt0) cc_final: 0.8721 (tt0) REVERT: F 619 ASP cc_start: 0.8508 (m-30) cc_final: 0.8255 (t0) REVERT: G 289 GLN cc_start: 0.8540 (tp40) cc_final: 0.8291 (tt0) REVERT: G 308 GLU cc_start: 0.8838 (tp30) cc_final: 0.8502 (mt-10) REVERT: G 312 GLN cc_start: 0.8992 (mt0) cc_final: 0.8743 (mt0) REVERT: G 314 ASP cc_start: 0.8375 (t0) cc_final: 0.8143 (t0) REVERT: G 412 MET cc_start: 0.8287 (mtp) cc_final: 0.7960 (mmp) REVERT: G 492 GLU cc_start: 0.8872 (tp30) cc_final: 0.8552 (tt0) REVERT: G 506 ASN cc_start: 0.8247 (t0) cc_final: 0.7728 (p0) REVERT: G 619 ASP cc_start: 0.8551 (m-30) cc_final: 0.8236 (t0) REVERT: H 314 ASP cc_start: 0.8129 (t0) cc_final: 0.7694 (t0) REVERT: H 412 MET cc_start: 0.7931 (mtp) cc_final: 0.7605 (mmt) REVERT: H 492 GLU cc_start: 0.8711 (tp30) cc_final: 0.8401 (tt0) REVERT: H 522 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8760 (tt0) REVERT: H 533 GLN cc_start: 0.8596 (mt0) cc_final: 0.8348 (tt0) REVERT: H 573 GLU cc_start: 0.8931 (tt0) cc_final: 0.8669 (mt-10) REVERT: H 618 MET cc_start: 0.8134 (mtp) cc_final: 0.7878 (mtp) REVERT: H 619 ASP cc_start: 0.8651 (m-30) cc_final: 0.8379 (t70) REVERT: I 241 ASN cc_start: 0.8399 (p0) cc_final: 0.7994 (m-40) REVERT: I 303 MET cc_start: 0.8307 (tpp) cc_final: 0.8062 (ttm) REVERT: I 308 GLU cc_start: 0.8727 (tp30) cc_final: 0.8209 (tp30) REVERT: I 312 GLN cc_start: 0.8831 (mt0) cc_final: 0.8287 (mt0) REVERT: I 314 ASP cc_start: 0.8513 (t0) cc_final: 0.8211 (t0) REVERT: I 412 MET cc_start: 0.8138 (mtp) cc_final: 0.7851 (mmp) REVERT: I 492 GLU cc_start: 0.8642 (tp30) cc_final: 0.8320 (tt0) REVERT: I 619 ASP cc_start: 0.8519 (m-30) cc_final: 0.8275 (t0) REVERT: J 265 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7711 (tt) REVERT: J 303 MET cc_start: 0.8304 (tpp) cc_final: 0.7818 (mtp) REVERT: J 412 MET cc_start: 0.8287 (mtp) cc_final: 0.8068 (mmt) REVERT: J 445 ASN cc_start: 0.8423 (m-40) cc_final: 0.8123 (m110) REVERT: J 492 GLU cc_start: 0.8618 (tp30) cc_final: 0.8319 (tt0) REVERT: J 501 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8362 (tm-30) REVERT: J 618 MET cc_start: 0.8356 (mtp) cc_final: 0.8075 (mtp) REVERT: J 619 ASP cc_start: 0.8587 (m-30) cc_final: 0.8355 (t0) REVERT: K 303 MET cc_start: 0.8174 (tpp) cc_final: 0.7934 (tpp) REVERT: K 308 GLU cc_start: 0.8810 (tt0) cc_final: 0.8504 (tp30) REVERT: K 312 GLN cc_start: 0.8673 (mt0) cc_final: 0.8437 (mt0) REVERT: K 314 ASP cc_start: 0.8446 (t0) cc_final: 0.8086 (t0) REVERT: K 412 MET cc_start: 0.8156 (mtp) cc_final: 0.7845 (mmp) REVERT: K 492 GLU cc_start: 0.8721 (tp30) cc_final: 0.8413 (tt0) REVERT: K 573 GLU cc_start: 0.8895 (tt0) cc_final: 0.8611 (mt-10) REVERT: K 619 ASP cc_start: 0.8306 (m-30) cc_final: 0.7986 (t70) REVERT: L 241 ASN cc_start: 0.8287 (p0) cc_final: 0.8024 (m-40) REVERT: L 314 ASP cc_start: 0.8240 (t0) cc_final: 0.7869 (t0) REVERT: L 412 MET cc_start: 0.8089 (mtp) cc_final: 0.7704 (mmt) REVERT: L 445 ASN cc_start: 0.8485 (m-40) cc_final: 0.8198 (m110) REVERT: L 492 GLU cc_start: 0.8643 (tp30) cc_final: 0.8373 (tt0) REVERT: L 501 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8147 (tm-30) REVERT: L 573 GLU cc_start: 0.8907 (tt0) cc_final: 0.8626 (mt-10) REVERT: L 619 ASP cc_start: 0.8460 (m-30) cc_final: 0.8211 (t0) REVERT: M 252 GLU cc_start: 0.9044 (tp30) cc_final: 0.8782 (pt0) REVERT: M 303 MET cc_start: 0.8381 (tpp) cc_final: 0.7851 (ttm) REVERT: M 307 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8009 (mt0) REVERT: M 308 GLU cc_start: 0.8699 (tt0) cc_final: 0.8466 (tp30) REVERT: M 412 MET cc_start: 0.8333 (mtp) cc_final: 0.7936 (mmp) REVERT: M 445 ASN cc_start: 0.8628 (m-40) cc_final: 0.8394 (m110) REVERT: M 533 GLN cc_start: 0.8611 (mt0) cc_final: 0.8333 (tt0) REVERT: M 573 GLU cc_start: 0.9036 (tt0) cc_final: 0.8749 (mt-10) REVERT: M 595 ILE cc_start: 0.8932 (mt) cc_final: 0.8619 (tp) REVERT: M 619 ASP cc_start: 0.8415 (m-30) cc_final: 0.8156 (t0) REVERT: N 303 MET cc_start: 0.8029 (tpt) cc_final: 0.7688 (tpp) REVERT: N 312 GLN cc_start: 0.8857 (mt0) cc_final: 0.8508 (mt0) REVERT: N 412 MET cc_start: 0.8234 (mtp) cc_final: 0.7932 (mmp) REVERT: N 445 ASN cc_start: 0.8589 (m-40) cc_final: 0.8229 (m110) REVERT: N 492 GLU cc_start: 0.8773 (tp30) cc_final: 0.8450 (tt0) REVERT: N 501 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8228 (tm-30) REVERT: N 506 ASN cc_start: 0.8377 (t0) cc_final: 0.7814 (p0) REVERT: N 533 GLN cc_start: 0.8636 (mt0) cc_final: 0.8379 (tt0) REVERT: N 573 GLU cc_start: 0.8982 (tp30) cc_final: 0.8644 (mt-10) REVERT: N 619 ASP cc_start: 0.8530 (m-30) cc_final: 0.8268 (t0) REVERT: O 308 GLU cc_start: 0.8697 (tt0) cc_final: 0.8492 (tp30) REVERT: O 327 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8788 (p) REVERT: O 412 MET cc_start: 0.8263 (mtp) cc_final: 0.7911 (mmp) REVERT: O 492 GLU cc_start: 0.8695 (tp30) cc_final: 0.8376 (tt0) REVERT: O 573 GLU cc_start: 0.8836 (tt0) cc_final: 0.8544 (mt-10) REVERT: O 590 MET cc_start: 0.8084 (ttm) cc_final: 0.7800 (tmm) REVERT: O 595 ILE cc_start: 0.8847 (mt) cc_final: 0.8590 (tp) REVERT: O 606 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8451 (mm-30) REVERT: O 619 ASP cc_start: 0.8526 (m-30) cc_final: 0.8263 (t0) outliers start: 181 outliers final: 82 residues processed: 1077 average time/residue: 0.5570 time to fit residues: 1052.3855 Evaluate side-chains 890 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 803 time to evaluate : 4.773 ------------------------------------------------------------------------------- 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 309 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 265 LEU 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 526 SER 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 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 449 SER Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 327 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 595 ILE Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 204 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 520 LYS 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 522 GLN Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 595 ILE Chi-restraints excluded: chain H residue 623 ILE Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 479 GLU 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 370 LYS 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 554 LEU Chi-restraints excluded: chain J residue 643 ILE Chi-restraints excluded: chain K residue 204 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 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 537 LEU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 204 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 426 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 415 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 0.4980 chunk 502 optimal weight: 20.0000 chunk 347 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 449 optimal weight: 9.9990 chunk 671 optimal weight: 1.9990 chunk 710 optimal weight: 7.9990 chunk 350 optimal weight: 8.9990 chunk 636 optimal weight: 10.0000 chunk 191 optimal weight: 0.6980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN D 408 ASN ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 HIS ** F 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 576 ASN J 408 ASN K 241 ASN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 ASN ** M 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 408 ASN O 340 GLN ** O 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 57015 Z= 0.425 Angle : 0.696 8.961 77175 Z= 0.353 Chirality : 0.048 0.210 9420 Planarity : 0.006 0.099 10065 Dihedral : 5.179 22.934 7875 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.57 % Favored : 91.22 % Rotamer: Outliers : 4.36 % Allowed : 15.57 % Favored : 80.06 % 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: -2.72 (0.09), residues: 7290 helix: -0.27 (0.11), residues: 2355 sheet: -2.59 (0.09), residues: 2670 loop : -2.07 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 341 HIS 0.006 0.001 HIS A 132 PHE 0.009 0.002 PHE H 642 TYR 0.022 0.002 TYR G 352 ARG 0.006 0.001 ARG H 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 1045 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 774 time to evaluate : 4.839 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8639 (t0) cc_final: 0.8262 (t0) REVERT: A 412 MET cc_start: 0.8116 (mtp) cc_final: 0.7704 (mmp) REVERT: A 445 ASN cc_start: 0.8559 (m-40) cc_final: 0.8177 (m110) REVERT: A 492 GLU cc_start: 0.8810 (tp30) cc_final: 0.8455 (tt0) REVERT: A 619 ASP cc_start: 0.8534 (m-30) cc_final: 0.8309 (t70) REVERT: B 308 GLU cc_start: 0.8751 (tp30) cc_final: 0.8525 (tp30) REVERT: B 312 GLN cc_start: 0.8875 (mt0) cc_final: 0.8580 (mt0) REVERT: B 412 MET cc_start: 0.8149 (mtp) cc_final: 0.7770 (mmt) REVERT: B 445 ASN cc_start: 0.8778 (m-40) cc_final: 0.8572 (m110) REVERT: B 492 GLU cc_start: 0.8916 (tp30) cc_final: 0.8635 (tt0) REVERT: B 501 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8709 (tm-30) REVERT: B 619 ASP cc_start: 0.8427 (m-30) cc_final: 0.8189 (t0) REVERT: C 412 MET cc_start: 0.8339 (mtp) cc_final: 0.8052 (mmp) REVERT: C 492 GLU cc_start: 0.8932 (tp30) cc_final: 0.8593 (tt0) REVERT: C 501 GLU cc_start: 0.8841 (mp0) cc_final: 0.8410 (tm-30) REVERT: C 590 MET cc_start: 0.8308 (ttm) cc_final: 0.8038 (tmm) REVERT: C 619 ASP cc_start: 0.8540 (m-30) cc_final: 0.8304 (t70) REVERT: D 308 GLU cc_start: 0.8769 (tp30) cc_final: 0.8560 (tp30) REVERT: D 312 GLN cc_start: 0.8991 (mt0) cc_final: 0.8731 (mt0) REVERT: D 327 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8789 (p) REVERT: D 412 MET cc_start: 0.8213 (mtp) cc_final: 0.7887 (mmp) REVERT: D 445 ASN cc_start: 0.8595 (m-40) cc_final: 0.8380 (m110) REVERT: D 492 GLU cc_start: 0.8912 (tp30) cc_final: 0.8600 (tt0) REVERT: D 501 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8437 (tm-30) REVERT: D 520 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8783 (ptmm) REVERT: D 573 GLU cc_start: 0.9008 (tt0) cc_final: 0.8738 (mt-10) REVERT: D 595 ILE cc_start: 0.8797 (mt) cc_final: 0.8510 (tp) REVERT: D 618 MET cc_start: 0.8204 (mtp) cc_final: 0.7977 (mtp) REVERT: D 619 ASP cc_start: 0.8416 (m-30) cc_final: 0.8139 (t0) REVERT: E 308 GLU cc_start: 0.8785 (tt0) cc_final: 0.8558 (tp30) REVERT: E 314 ASP cc_start: 0.8688 (t0) cc_final: 0.8319 (t0) REVERT: E 492 GLU cc_start: 0.8749 (tp30) cc_final: 0.8412 (tt0) REVERT: E 501 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8543 (tm-30) REVERT: E 619 ASP cc_start: 0.8081 (m-30) cc_final: 0.7848 (t70) REVERT: F 314 ASP cc_start: 0.8452 (t0) cc_final: 0.8156 (t0) REVERT: F 412 MET cc_start: 0.7994 (mtp) cc_final: 0.7766 (mmp) REVERT: F 445 ASN cc_start: 0.8750 (m-40) cc_final: 0.8375 (m110) REVERT: F 492 GLU cc_start: 0.8919 (tp30) cc_final: 0.8624 (tt0) REVERT: F 590 MET cc_start: 0.7997 (tmm) cc_final: 0.7666 (mpp) REVERT: F 619 ASP cc_start: 0.8472 (m-30) cc_final: 0.8217 (t0) REVERT: G 314 ASP cc_start: 0.8577 (t0) cc_final: 0.8089 (t0) REVERT: G 412 MET cc_start: 0.8357 (mtp) cc_final: 0.7921 (mmp) REVERT: G 492 GLU cc_start: 0.8991 (tp30) cc_final: 0.8695 (tt0) REVERT: G 619 ASP cc_start: 0.8708 (m-30) cc_final: 0.8399 (t0) REVERT: H 314 ASP cc_start: 0.8466 (t0) cc_final: 0.8178 (t0) REVERT: H 412 MET cc_start: 0.7758 (mtp) cc_final: 0.7447 (mmt) REVERT: H 492 GLU cc_start: 0.8874 (tp30) cc_final: 0.8557 (tt0) REVERT: H 533 GLN cc_start: 0.8564 (mt0) cc_final: 0.8268 (tt0) REVERT: H 618 MET cc_start: 0.8221 (mtp) cc_final: 0.7999 (mtp) REVERT: H 619 ASP cc_start: 0.8678 (m-30) cc_final: 0.8437 (t70) REVERT: I 303 MET cc_start: 0.8378 (tpp) cc_final: 0.8112 (tpp) REVERT: I 308 GLU cc_start: 0.8774 (tp30) cc_final: 0.8256 (tp30) REVERT: I 312 GLN cc_start: 0.8947 (mt0) cc_final: 0.8310 (mt0) REVERT: I 314 ASP cc_start: 0.8687 (t0) cc_final: 0.8262 (t0) REVERT: I 412 MET cc_start: 0.8090 (mtp) cc_final: 0.7794 (mmp) REVERT: I 445 ASN cc_start: 0.8994 (m-40) cc_final: 0.8709 (m110) REVERT: I 492 GLU cc_start: 0.8857 (tp30) cc_final: 0.8549 (tt0) REVERT: I 619 ASP cc_start: 0.8430 (m-30) cc_final: 0.8202 (t70) REVERT: I 620 ASP cc_start: 0.8422 (m-30) cc_final: 0.7641 (p0) REVERT: I 635 HIS cc_start: 0.8229 (OUTLIER) cc_final: 0.8018 (t-90) REVERT: J 303 MET cc_start: 0.8359 (tpp) cc_final: 0.8138 (tpp) REVERT: J 412 MET cc_start: 0.8345 (mtp) cc_final: 0.8099 (mmp) REVERT: J 445 ASN cc_start: 0.8600 (m-40) cc_final: 0.8260 (m110) REVERT: J 492 GLU cc_start: 0.8788 (tp30) cc_final: 0.8511 (tt0) REVERT: J 619 ASP cc_start: 0.8608 (m-30) cc_final: 0.8384 (t0) REVERT: K 303 MET cc_start: 0.8262 (tpp) cc_final: 0.8040 (tpp) REVERT: K 308 GLU cc_start: 0.8833 (tt0) cc_final: 0.8627 (tp30) REVERT: K 314 ASP cc_start: 0.8658 (t0) cc_final: 0.8296 (t0) REVERT: K 412 MET cc_start: 0.8078 (mtp) cc_final: 0.7810 (mmp) REVERT: K 492 GLU cc_start: 0.8913 (tp30) cc_final: 0.8631 (tt0) REVERT: K 619 ASP cc_start: 0.8076 (m-30) cc_final: 0.7778 (t70) REVERT: L 303 MET cc_start: 0.8341 (mmm) cc_final: 0.8106 (tpp) REVERT: L 308 GLU cc_start: 0.8621 (tt0) cc_final: 0.8198 (tm-30) REVERT: L 314 ASP cc_start: 0.8575 (t0) cc_final: 0.8351 (t0) REVERT: L 412 MET cc_start: 0.7984 (mtp) cc_final: 0.7641 (mmt) REVERT: L 445 ASN cc_start: 0.8616 (m-40) cc_final: 0.8293 (m110) REVERT: L 492 GLU cc_start: 0.8791 (tp30) cc_final: 0.8533 (tt0) REVERT: L 573 GLU cc_start: 0.8901 (tt0) cc_final: 0.8607 (mt-10) REVERT: L 619 ASP cc_start: 0.8409 (m-30) cc_final: 0.8144 (t0) REVERT: M 252 GLU cc_start: 0.9106 (tp30) cc_final: 0.8851 (pt0) REVERT: M 303 MET cc_start: 0.8515 (tpp) cc_final: 0.8130 (ttm) REVERT: M 307 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8168 (mt0) REVERT: M 308 GLU cc_start: 0.8717 (tt0) cc_final: 0.8482 (tp30) REVERT: M 412 MET cc_start: 0.8319 (mtp) cc_final: 0.7920 (mmp) REVERT: M 445 ASN cc_start: 0.8853 (m-40) cc_final: 0.8579 (m110) REVERT: M 533 GLN cc_start: 0.8592 (mt0) cc_final: 0.8295 (tt0) REVERT: M 573 GLU cc_start: 0.9021 (tt0) cc_final: 0.8745 (mt-10) REVERT: M 619 ASP cc_start: 0.8332 (m-30) cc_final: 0.8104 (t0) REVERT: N 327 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8924 (p) REVERT: N 412 MET cc_start: 0.8185 (mtp) cc_final: 0.7885 (mmp) REVERT: N 445 ASN cc_start: 0.8662 (m-40) cc_final: 0.8325 (m110) REVERT: N 492 GLU cc_start: 0.8923 (tp30) cc_final: 0.8616 (tt0) REVERT: N 501 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8487 (tm-30) REVERT: N 506 ASN cc_start: 0.8588 (t0) cc_final: 0.8030 (p0) REVERT: N 590 MET cc_start: 0.8221 (ttm) cc_final: 0.7948 (tmm) REVERT: N 619 ASP cc_start: 0.8434 (m-30) cc_final: 0.8205 (t70) REVERT: O 308 GLU cc_start: 0.8729 (tt0) cc_final: 0.8514 (tp30) REVERT: O 314 ASP cc_start: 0.8467 (t0) cc_final: 0.8207 (t0) REVERT: O 327 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8766 (p) REVERT: O 412 MET cc_start: 0.8182 (mtp) cc_final: 0.7848 (mmp) REVERT: O 492 GLU cc_start: 0.8806 (tp30) cc_final: 0.8496 (tt0) REVERT: O 573 GLU cc_start: 0.8882 (tt0) cc_final: 0.8589 (mt-10) REVERT: O 590 MET cc_start: 0.8089 (ttm) cc_final: 0.7807 (tmm) REVERT: O 595 ILE cc_start: 0.8861 (mt) cc_final: 0.8532 (tp) REVERT: O 606 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8333 (mm-30) REVERT: O 619 ASP cc_start: 0.8414 (m-30) cc_final: 0.8145 (t0) outliers start: 271 outliers final: 149 residues processed: 991 average time/residue: 0.4875 time to fit residues: 848.1482 Evaluate side-chains 847 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 694 time to evaluate : 4.732 ------------------------------------------------------------------------------- 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 449 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain B residue 204 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 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 C residue 117 LEU 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 D residue 204 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 323 GLU 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 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 635 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 309 VAL 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 536 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 327 VAL 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 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 449 SER 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 595 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 345 GLU Chi-restraints excluded: chain H residue 426 VAL 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 536 VAL Chi-restraints excluded: chain H residue 554 LEU 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 246 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 351 GLN 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 479 GLU Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 635 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 370 LYS 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 485 LYS Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 564 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 451 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 635 HIS Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 265 LEU 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 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 246 LEU Chi-restraints excluded: chain M residue 309 VAL Chi-restraints excluded: chain M residue 323 GLU Chi-restraints excluded: chain M residue 363 MET Chi-restraints excluded: chain M residue 415 VAL 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 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 327 VAL Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 439 SER 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 117 LEU 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 439 SER 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: 6.9990 chunk 10 optimal weight: 9.9990 chunk 528 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 chunk 606 optimal weight: 0.5980 chunk 491 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 362 optimal weight: 5.9990 chunk 637 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN D 601 ASN ** F 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 524 ASN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 524 ASN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 57015 Z= 0.308 Angle : 0.621 9.027 77175 Z= 0.315 Chirality : 0.047 0.210 9420 Planarity : 0.006 0.096 10065 Dihedral : 4.903 22.328 7875 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.43 % Favored : 93.36 % Rotamer: Outliers : 3.83 % Allowed : 17.55 % Favored : 78.62 % 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: -2.45 (0.09), residues: 7290 helix: 0.07 (0.11), residues: 2295 sheet: -2.50 (0.09), residues: 2670 loop : -1.91 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 341 HIS 0.004 0.001 HIS A 132 PHE 0.009 0.001 PHE N 642 TYR 0.021 0.002 TYR G 352 ARG 0.006 0.000 ARG F 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 1016 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 778 time to evaluate : 4.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8603 (t0) cc_final: 0.8186 (t0) REVERT: A 412 MET cc_start: 0.8143 (mtp) cc_final: 0.7860 (mmp) REVERT: A 445 ASN cc_start: 0.8543 (m-40) cc_final: 0.8170 (m110) REVERT: A 492 GLU cc_start: 0.8778 (tp30) cc_final: 0.8409 (tt0) REVERT: A 619 ASP cc_start: 0.8463 (m-30) cc_final: 0.8251 (t70) REVERT: A 620 ASP cc_start: 0.8576 (m-30) cc_final: 0.7816 (p0) REVERT: B 308 GLU cc_start: 0.8690 (tp30) cc_final: 0.8468 (tp30) REVERT: B 312 GLN cc_start: 0.8739 (mt0) cc_final: 0.8451 (mt0) REVERT: B 412 MET cc_start: 0.8110 (mtp) cc_final: 0.7796 (mmp) REVERT: B 445 ASN cc_start: 0.8753 (m-40) cc_final: 0.8522 (m110) REVERT: B 492 GLU cc_start: 0.8905 (tp30) cc_final: 0.8620 (tt0) REVERT: B 501 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8698 (tm-30) REVERT: B 506 ASN cc_start: 0.8545 (t0) cc_final: 0.8288 (p0) REVERT: B 619 ASP cc_start: 0.8160 (m-30) cc_final: 0.7894 (t0) REVERT: C 412 MET cc_start: 0.8275 (mtp) cc_final: 0.7972 (mmp) REVERT: C 492 GLU cc_start: 0.8909 (tp30) cc_final: 0.8639 (tt0) REVERT: C 546 LEU cc_start: 0.9355 (mp) cc_final: 0.8977 (tp) REVERT: C 619 ASP cc_start: 0.8691 (m-30) cc_final: 0.8462 (t70) REVERT: D 308 GLU cc_start: 0.8722 (tp30) cc_final: 0.8399 (tt0) REVERT: D 312 GLN cc_start: 0.8949 (mt0) cc_final: 0.8690 (mt0) REVERT: D 327 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8767 (p) REVERT: D 412 MET cc_start: 0.8288 (mtp) cc_final: 0.7926 (mmp) REVERT: D 414 LEU cc_start: 0.8266 (mm) cc_final: 0.8056 (pp) REVERT: D 445 ASN cc_start: 0.8591 (m-40) cc_final: 0.8303 (m110) REVERT: D 492 GLU cc_start: 0.8893 (tp30) cc_final: 0.8608 (tt0) REVERT: D 573 GLU cc_start: 0.8835 (tt0) cc_final: 0.8573 (mt-10) REVERT: D 595 ILE cc_start: 0.8777 (mt) cc_final: 0.8486 (tp) REVERT: D 619 ASP cc_start: 0.8328 (m-30) cc_final: 0.8047 (t0) REVERT: E 314 ASP cc_start: 0.8725 (t0) cc_final: 0.8316 (t0) REVERT: E 492 GLU cc_start: 0.8707 (tp30) cc_final: 0.8352 (tt0) REVERT: E 501 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8497 (tm-30) REVERT: E 506 ASN cc_start: 0.8446 (t0) cc_final: 0.8024 (p0) REVERT: E 619 ASP cc_start: 0.7960 (m-30) cc_final: 0.7731 (t70) REVERT: F 314 ASP cc_start: 0.8388 (t0) cc_final: 0.7905 (t0) REVERT: F 412 MET cc_start: 0.7989 (mtp) cc_final: 0.7746 (mmp) REVERT: F 445 ASN cc_start: 0.8828 (m-40) cc_final: 0.8456 (m110) REVERT: F 492 GLU cc_start: 0.8871 (tp30) cc_final: 0.8571 (tt0) REVERT: F 506 ASN cc_start: 0.8513 (t0) cc_final: 0.7844 (p0) REVERT: F 590 MET cc_start: 0.7966 (tmm) cc_final: 0.7635 (mpp) REVERT: F 619 ASP cc_start: 0.8379 (m-30) cc_final: 0.8131 (t0) REVERT: G 312 GLN cc_start: 0.9024 (mt0) cc_final: 0.8721 (mt0) REVERT: G 314 ASP cc_start: 0.8603 (t0) cc_final: 0.8356 (t0) REVERT: G 412 MET cc_start: 0.8313 (mtp) cc_final: 0.7898 (mmp) REVERT: G 492 GLU cc_start: 0.8960 (tp30) cc_final: 0.8643 (tt0) REVERT: G 619 ASP cc_start: 0.8509 (m-30) cc_final: 0.8173 (t0) REVERT: H 314 ASP cc_start: 0.8455 (t0) cc_final: 0.8102 (t0) REVERT: H 412 MET cc_start: 0.7759 (mtp) cc_final: 0.7438 (mmt) REVERT: H 492 GLU cc_start: 0.8787 (tp30) cc_final: 0.8468 (tt0) REVERT: H 533 GLN cc_start: 0.8548 (mt0) cc_final: 0.8316 (tt0) REVERT: H 618 MET cc_start: 0.8142 (mtp) cc_final: 0.7896 (mtp) REVERT: H 619 ASP cc_start: 0.8742 (m-30) cc_final: 0.8505 (t70) REVERT: I 308 GLU cc_start: 0.8770 (tp30) cc_final: 0.8301 (tp30) REVERT: I 312 GLN cc_start: 0.9006 (mt0) cc_final: 0.8537 (mt0) REVERT: I 314 ASP cc_start: 0.8665 (t0) cc_final: 0.8187 (t0) REVERT: I 412 MET cc_start: 0.8140 (mtp) cc_final: 0.7859 (mmp) REVERT: I 492 GLU cc_start: 0.8837 (tp30) cc_final: 0.8498 (tt0) REVERT: I 551 LYS cc_start: 0.8823 (pttt) cc_final: 0.8618 (pttp) REVERT: I 619 ASP cc_start: 0.8298 (m-30) cc_final: 0.8069 (t70) REVERT: I 620 ASP cc_start: 0.8402 (m-30) cc_final: 0.7637 (p0) REVERT: I 635 HIS cc_start: 0.8238 (m-70) cc_final: 0.8011 (t-90) REVERT: J 132 HIS cc_start: 0.2752 (OUTLIER) cc_final: 0.2415 (t-90) REVERT: J 303 MET cc_start: 0.8435 (tpp) cc_final: 0.8219 (tpp) REVERT: J 314 ASP cc_start: 0.8325 (t0) cc_final: 0.7998 (t0) REVERT: J 412 MET cc_start: 0.8267 (mtp) cc_final: 0.7899 (mmp) REVERT: J 445 ASN cc_start: 0.8501 (m-40) cc_final: 0.8139 (m110) REVERT: J 492 GLU cc_start: 0.8731 (tp30) cc_final: 0.8454 (tt0) REVERT: J 619 ASP cc_start: 0.8546 (m-30) cc_final: 0.8315 (t0) REVERT: K 303 MET cc_start: 0.8288 (tpp) cc_final: 0.8039 (tpp) REVERT: K 308 GLU cc_start: 0.8793 (tt0) cc_final: 0.8577 (tp30) REVERT: K 314 ASP cc_start: 0.8477 (t0) cc_final: 0.8099 (t0) REVERT: K 412 MET cc_start: 0.8085 (mtp) cc_final: 0.7798 (mmp) REVERT: K 492 GLU cc_start: 0.8873 (tp30) cc_final: 0.8600 (tt0) REVERT: K 619 ASP cc_start: 0.8110 (m-30) cc_final: 0.7809 (t70) REVERT: L 132 HIS cc_start: 0.3564 (OUTLIER) cc_final: 0.3172 (t70) REVERT: L 303 MET cc_start: 0.8275 (mmm) cc_final: 0.8057 (tpp) REVERT: L 314 ASP cc_start: 0.8583 (t0) cc_final: 0.8321 (t0) REVERT: L 412 MET cc_start: 0.7917 (mtp) cc_final: 0.7574 (mmt) REVERT: L 445 ASN cc_start: 0.8685 (m-40) cc_final: 0.8374 (m110) REVERT: L 492 GLU cc_start: 0.8766 (tp30) cc_final: 0.8478 (tt0) REVERT: L 619 ASP cc_start: 0.8255 (m-30) cc_final: 0.7965 (t0) REVERT: M 132 HIS cc_start: 0.2720 (OUTLIER) cc_final: 0.2278 (t70) REVERT: M 252 GLU cc_start: 0.9026 (tp30) cc_final: 0.8735 (pt0) REVERT: M 303 MET cc_start: 0.8476 (tpp) cc_final: 0.7947 (ttm) REVERT: M 307 GLN cc_start: 0.8559 (tp-100) cc_final: 0.7955 (mt0) REVERT: M 308 GLU cc_start: 0.8680 (tt0) cc_final: 0.8423 (tp30) REVERT: M 412 MET cc_start: 0.8283 (mtp) cc_final: 0.7894 (mmp) REVERT: M 445 ASN cc_start: 0.8873 (m-40) cc_final: 0.8590 (m110) REVERT: M 506 ASN cc_start: 0.8440 (t0) cc_final: 0.8181 (p0) REVERT: M 533 GLN cc_start: 0.8545 (mt0) cc_final: 0.8279 (tt0) REVERT: M 573 GLU cc_start: 0.8988 (tt0) cc_final: 0.8714 (mt-10) REVERT: M 619 ASP cc_start: 0.8224 (m-30) cc_final: 0.7957 (t70) REVERT: N 327 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8856 (p) REVERT: N 412 MET cc_start: 0.8181 (mtp) cc_final: 0.7892 (mmp) REVERT: N 445 ASN cc_start: 0.8534 (m-40) cc_final: 0.8190 (m110) REVERT: N 492 GLU cc_start: 0.8834 (tp30) cc_final: 0.8515 (tt0) REVERT: N 501 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8393 (tm-30) REVERT: N 573 GLU cc_start: 0.8983 (tp30) cc_final: 0.8675 (mt-10) REVERT: N 619 ASP cc_start: 0.8381 (m-30) cc_final: 0.8136 (t0) REVERT: O 308 GLU cc_start: 0.8728 (tt0) cc_final: 0.8522 (tp30) REVERT: O 327 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8736 (p) REVERT: O 412 MET cc_start: 0.8211 (mtp) cc_final: 0.7896 (mmp) REVERT: O 492 GLU cc_start: 0.8768 (tp30) cc_final: 0.8414 (tt0) REVERT: O 534 MET cc_start: 0.8937 (ttm) cc_final: 0.8720 (mtp) REVERT: O 573 GLU cc_start: 0.8840 (tt0) cc_final: 0.8562 (mt-10) REVERT: O 595 ILE cc_start: 0.8757 (mt) cc_final: 0.8498 (tp) REVERT: O 619 ASP cc_start: 0.8324 (m-30) cc_final: 0.8051 (t0) outliers start: 238 outliers final: 149 residues processed: 976 average time/residue: 0.4923 time to fit residues: 843.0520 Evaluate side-chains 841 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 686 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU 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 449 SER 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 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 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 449 SER 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 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 415 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 554 LEU 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 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 451 ILE 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 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 257 VAL Chi-restraints excluded: chain F residue 265 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 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 243 VAL Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 595 ILE 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 415 VAL Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 595 ILE Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 265 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 479 GLU Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 554 LEU Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain J residue 117 LEU 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 370 LYS 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 564 LEU Chi-restraints excluded: chain K residue 117 LEU 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 451 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 603 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 514 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 537 LEU 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 246 LEU 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 M residue 546 LEU Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 554 LEU Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 635 HIS 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 439 SER Chi-restraints excluded: chain O residue 603 ILE Chi-restraints excluded: chain O residue 635 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 6.9990 chunk 639 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 417 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 711 optimal weight: 7.9990 chunk 590 optimal weight: 5.9990 chunk 329 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 373 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** F 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 ASN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 635 HIS M 340 GLN ** M 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 57015 Z= 0.444 Angle : 0.692 9.074 77175 Z= 0.351 Chirality : 0.048 0.214 9420 Planarity : 0.006 0.094 10065 Dihedral : 5.076 23.102 7875 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.41 % Favored : 90.38 % Rotamer: Outliers : 5.04 % Allowed : 17.20 % Favored : 77.76 % 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: -2.56 (0.10), residues: 7290 helix: 0.09 (0.11), residues: 2280 sheet: -2.67 (0.10), residues: 2475 loop : -2.07 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 341 HIS 0.007 0.002 HIS B 635 PHE 0.012 0.002 PHE E 642 TYR 0.025 0.002 TYR G 352 ARG 0.007 0.001 ARG B 181 *********************** 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 1034 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 721 time to evaluate : 4.753 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8680 (t0) cc_final: 0.8309 (t0) REVERT: A 412 MET cc_start: 0.8083 (mtp) cc_final: 0.7865 (mmt) REVERT: A 445 ASN cc_start: 0.8702 (m-40) cc_final: 0.8343 (m110) REVERT: A 492 GLU cc_start: 0.8840 (tp30) cc_final: 0.8512 (tt0) REVERT: A 619 ASP cc_start: 0.8456 (m-30) cc_final: 0.8247 (t70) REVERT: A 620 ASP cc_start: 0.8652 (m-30) cc_final: 0.7803 (p0) REVERT: B 132 HIS cc_start: 0.2967 (OUTLIER) cc_final: 0.2658 (t70) REVERT: B 312 GLN cc_start: 0.8733 (mt0) cc_final: 0.8462 (mt0) REVERT: B 412 MET cc_start: 0.8158 (mtp) cc_final: 0.7852 (mmp) REVERT: B 445 ASN cc_start: 0.8857 (m-40) cc_final: 0.8627 (m110) REVERT: B 492 GLU cc_start: 0.8943 (tp30) cc_final: 0.8657 (tt0) REVERT: B 506 ASN cc_start: 0.8656 (t0) cc_final: 0.8270 (p0) REVERT: B 619 ASP cc_start: 0.8266 (m-30) cc_final: 0.8017 (t0) REVERT: C 412 MET cc_start: 0.8369 (mtp) cc_final: 0.8001 (mmp) REVERT: C 492 GLU cc_start: 0.8962 (tp30) cc_final: 0.8669 (tt0) REVERT: C 501 GLU cc_start: 0.8844 (mp0) cc_final: 0.8424 (tm-30) REVERT: C 546 LEU cc_start: 0.9368 (mp) cc_final: 0.8999 (tp) REVERT: C 590 MET cc_start: 0.8241 (ttm) cc_final: 0.7979 (tmm) REVERT: C 619 ASP cc_start: 0.8561 (m-30) cc_final: 0.8306 (t70) REVERT: D 308 GLU cc_start: 0.8758 (tp30) cc_final: 0.8488 (tt0) REVERT: D 312 GLN cc_start: 0.8914 (mt0) cc_final: 0.8625 (mt0) REVERT: D 327 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8825 (p) REVERT: D 412 MET cc_start: 0.8331 (mtp) cc_final: 0.7988 (mmp) REVERT: D 492 GLU cc_start: 0.8899 (tp30) cc_final: 0.8606 (tt0) REVERT: D 595 ILE cc_start: 0.8773 (mt) cc_final: 0.8481 (tp) REVERT: D 619 ASP cc_start: 0.8020 (m-30) cc_final: 0.7772 (t0) REVERT: E 132 HIS cc_start: 0.3423 (OUTLIER) cc_final: 0.3086 (t70) REVERT: E 133 TYR cc_start: 0.3738 (p90) cc_final: 0.3488 (p90) REVERT: E 314 ASP cc_start: 0.8727 (t0) cc_final: 0.8367 (t0) REVERT: E 492 GLU cc_start: 0.8821 (tp30) cc_final: 0.8516 (tt0) REVERT: E 501 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8602 (tm-30) REVERT: E 506 ASN cc_start: 0.8615 (t0) cc_final: 0.8228 (p0) REVERT: E 619 ASP cc_start: 0.7952 (m-30) cc_final: 0.7714 (t70) REVERT: F 132 HIS cc_start: 0.3389 (OUTLIER) cc_final: 0.3037 (t70) REVERT: F 314 ASP cc_start: 0.8523 (t0) cc_final: 0.8194 (t0) REVERT: F 412 MET cc_start: 0.8025 (mtp) cc_final: 0.7782 (mmp) REVERT: F 492 GLU cc_start: 0.8923 (tp30) cc_final: 0.8643 (tt0) REVERT: F 501 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8051 (mp0) REVERT: F 590 MET cc_start: 0.7967 (tmm) cc_final: 0.7632 (mpp) REVERT: F 619 ASP cc_start: 0.8365 (m-30) cc_final: 0.8098 (t0) REVERT: G 314 ASP cc_start: 0.8690 (t0) cc_final: 0.8384 (t0) REVERT: G 412 MET cc_start: 0.8317 (mtp) cc_final: 0.7886 (mmp) REVERT: G 492 GLU cc_start: 0.9004 (tp30) cc_final: 0.8700 (tt0) REVERT: G 619 ASP cc_start: 0.8514 (m-30) cc_final: 0.8205 (t0) REVERT: H 312 GLN cc_start: 0.8913 (mt0) cc_final: 0.8637 (mt0) REVERT: H 314 ASP cc_start: 0.8533 (t0) cc_final: 0.8189 (t0) REVERT: H 412 MET cc_start: 0.7795 (mtp) cc_final: 0.7461 (mmp) REVERT: H 492 GLU cc_start: 0.8910 (tp30) cc_final: 0.8595 (tt0) REVERT: H 533 GLN cc_start: 0.8446 (mt0) cc_final: 0.8214 (tt0) REVERT: H 618 MET cc_start: 0.8266 (mtp) cc_final: 0.8043 (mtp) REVERT: H 619 ASP cc_start: 0.8874 (m-30) cc_final: 0.8660 (t0) REVERT: I 132 HIS cc_start: 0.2861 (OUTLIER) cc_final: 0.2497 (t70) REVERT: I 314 ASP cc_start: 0.8723 (t0) cc_final: 0.8263 (t0) REVERT: I 412 MET cc_start: 0.8243 (mtp) cc_final: 0.7932 (mmp) REVERT: I 492 GLU cc_start: 0.8872 (tp30) cc_final: 0.8554 (tt0) REVERT: I 619 ASP cc_start: 0.8171 (m-30) cc_final: 0.7925 (t70) REVERT: I 635 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7964 (t-90) REVERT: J 412 MET cc_start: 0.8325 (mtp) cc_final: 0.7920 (mmp) REVERT: J 445 ASN cc_start: 0.8436 (m-40) cc_final: 0.8109 (m110) REVERT: J 492 GLU cc_start: 0.8826 (tp30) cc_final: 0.8538 (tt0) REVERT: J 618 MET cc_start: 0.8512 (mtp) cc_final: 0.8165 (mtp) REVERT: J 619 ASP cc_start: 0.8655 (m-30) cc_final: 0.8442 (t0) REVERT: K 314 ASP cc_start: 0.8663 (t0) cc_final: 0.8311 (t0) REVERT: K 412 MET cc_start: 0.8152 (mtp) cc_final: 0.7886 (mmp) REVERT: K 492 GLU cc_start: 0.8928 (tp30) cc_final: 0.8651 (tt0) REVERT: K 619 ASP cc_start: 0.8127 (m-30) cc_final: 0.7832 (t70) REVERT: L 303 MET cc_start: 0.8345 (mmm) cc_final: 0.8105 (tpp) REVERT: L 314 ASP cc_start: 0.8688 (t0) cc_final: 0.8424 (t0) REVERT: L 412 MET cc_start: 0.7968 (mtp) cc_final: 0.7630 (mmt) REVERT: L 492 GLU cc_start: 0.8829 (tp30) cc_final: 0.8572 (tt0) REVERT: L 546 LEU cc_start: 0.9270 (mp) cc_final: 0.8952 (tt) REVERT: L 619 ASP cc_start: 0.8226 (m-30) cc_final: 0.7983 (t0) REVERT: L 620 ASP cc_start: 0.8613 (m-30) cc_final: 0.8051 (p0) REVERT: L 634 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8547 (ttp-170) REVERT: L 635 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7915 (t70) REVERT: M 132 HIS cc_start: 0.2730 (OUTLIER) cc_final: 0.2363 (t70) REVERT: M 252 GLU cc_start: 0.9068 (tp30) cc_final: 0.8783 (pt0) REVERT: M 303 MET cc_start: 0.8493 (tpp) cc_final: 0.7911 (ttm) REVERT: M 307 GLN cc_start: 0.8582 (tp-100) cc_final: 0.7959 (mt0) REVERT: M 308 GLU cc_start: 0.8660 (tt0) cc_final: 0.8408 (tp30) REVERT: M 412 MET cc_start: 0.8324 (mtp) cc_final: 0.7944 (mmp) REVERT: M 445 ASN cc_start: 0.8881 (m-40) cc_final: 0.8571 (m110) REVERT: M 533 GLN cc_start: 0.8493 (mt0) cc_final: 0.8232 (tt0) REVERT: M 573 GLU cc_start: 0.8972 (tt0) cc_final: 0.8684 (mt-10) REVERT: M 619 ASP cc_start: 0.8138 (m-30) cc_final: 0.7875 (t0) REVERT: N 412 MET cc_start: 0.8211 (mtp) cc_final: 0.7926 (mmp) REVERT: N 492 GLU cc_start: 0.8843 (tp30) cc_final: 0.8539 (tt0) REVERT: N 506 ASN cc_start: 0.8549 (t0) cc_final: 0.8025 (p0) REVERT: N 575 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8457 (ttmm) REVERT: N 590 MET cc_start: 0.8269 (ttm) cc_final: 0.8015 (tmm) REVERT: N 613 GLN cc_start: 0.7827 (mt0) cc_final: 0.7224 (pp30) REVERT: N 619 ASP cc_start: 0.8314 (m-30) cc_final: 0.8064 (t0) REVERT: O 327 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8763 (p) REVERT: O 412 MET cc_start: 0.8240 (mtp) cc_final: 0.7934 (mmp) REVERT: O 492 GLU cc_start: 0.8831 (tp30) cc_final: 0.8493 (tt0) REVERT: O 573 GLU cc_start: 0.8830 (tt0) cc_final: 0.8570 (mt-10) REVERT: O 590 MET cc_start: 0.8007 (ttm) cc_final: 0.7769 (tmm) REVERT: O 619 ASP cc_start: 0.8297 (m-30) cc_final: 0.8010 (t0) outliers start: 313 outliers final: 213 residues processed: 971 average time/residue: 0.4846 time to fit residues: 826.7496 Evaluate side-chains 898 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 676 time to evaluate : 4.664 ------------------------------------------------------------------------------- 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 439 SER Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 VAL 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 254 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 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 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 534 MET 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 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 404 LEU 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 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 D residue 204 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 323 GLU 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 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 603 ILE Chi-restraints excluded: chain D residue 635 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 309 VAL 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 449 SER Chi-restraints excluded: chain E residue 451 ILE 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 257 VAL Chi-restraints excluded: chain F residue 265 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 449 SER Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 524 ASN 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 243 VAL Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 370 LYS 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 529 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 603 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 345 GLU Chi-restraints excluded: chain H residue 415 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 536 VAL Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 595 ILE 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 132 HIS 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 351 GLN 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 479 GLU Chi-restraints excluded: chain I residue 595 ILE 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 363 MET Chi-restraints excluded: chain J residue 370 LYS 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 529 VAL Chi-restraints excluded: chain J residue 564 LEU 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 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 451 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 603 ILE 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 480 VAL Chi-restraints excluded: chain L residue 514 VAL 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 L residue 635 HIS Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 158 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 426 VAL Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 480 VAL Chi-restraints excluded: chain M residue 534 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 546 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 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 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 439 SER Chi-restraints excluded: chain O residue 449 SER Chi-restraints excluded: chain O residue 547 GLU 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: 3.9990 chunk 80 optimal weight: 0.9990 chunk 405 optimal weight: 0.5980 chunk 519 optimal weight: 2.9990 chunk 402 optimal weight: 0.9990 chunk 598 optimal weight: 7.9990 chunk 397 optimal weight: 7.9990 chunk 708 optimal weight: 1.9990 chunk 443 optimal weight: 8.9990 chunk 431 optimal weight: 4.9990 chunk 327 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 524 ASN L 408 ASN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 57015 Z= 0.236 Angle : 0.597 8.231 77175 Z= 0.305 Chirality : 0.046 0.201 9420 Planarity : 0.005 0.092 10065 Dihedral : 4.716 23.106 7875 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.03 % Favored : 94.76 % Rotamer: Outliers : 3.46 % Allowed : 19.50 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.10), residues: 7290 helix: 0.29 (0.11), residues: 2295 sheet: -2.55 (0.10), residues: 2535 loop : -1.93 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 341 HIS 0.003 0.001 HIS J 635 PHE 0.009 0.001 PHE J 642 TYR 0.021 0.001 TYR J 352 ARG 0.009 0.000 ARG B 181 *********************** 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 967 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 752 time to evaluate : 4.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8539 (t0) cc_final: 0.8089 (t0) REVERT: A 412 MET cc_start: 0.8058 (mtp) cc_final: 0.7844 (mmp) REVERT: A 445 ASN cc_start: 0.8497 (m-40) cc_final: 0.8126 (m110) REVERT: A 492 GLU cc_start: 0.8808 (tp30) cc_final: 0.8477 (tt0) REVERT: A 506 ASN cc_start: 0.8606 (t0) cc_final: 0.8194 (p0) REVERT: A 619 ASP cc_start: 0.8380 (m-30) cc_final: 0.8107 (t70) REVERT: A 620 ASP cc_start: 0.8471 (m-30) cc_final: 0.7686 (p0) REVERT: B 132 HIS cc_start: 0.2840 (OUTLIER) cc_final: 0.2540 (t70) REVERT: B 312 GLN cc_start: 0.8630 (mt0) cc_final: 0.8352 (mt0) REVERT: B 412 MET cc_start: 0.8089 (mtp) cc_final: 0.7798 (mmp) REVERT: B 445 ASN cc_start: 0.8669 (m-40) cc_final: 0.8400 (m110) REVERT: B 492 GLU cc_start: 0.8866 (tp30) cc_final: 0.8576 (tt0) REVERT: B 501 GLU cc_start: 0.8773 (mp0) cc_final: 0.8428 (tm-30) REVERT: B 619 ASP cc_start: 0.8054 (m-30) cc_final: 0.7795 (t0) REVERT: C 412 MET cc_start: 0.8393 (mtp) cc_final: 0.8143 (mmp) REVERT: C 492 GLU cc_start: 0.8921 (tp30) cc_final: 0.8607 (tt0) REVERT: C 501 GLU cc_start: 0.8494 (mp0) cc_final: 0.8137 (tm-30) REVERT: C 506 ASN cc_start: 0.8471 (t0) cc_final: 0.7938 (p0) REVERT: C 546 LEU cc_start: 0.9427 (mp) cc_final: 0.9105 (tp) REVERT: C 619 ASP cc_start: 0.8583 (m-30) cc_final: 0.8350 (t70) REVERT: C 634 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8607 (ttp-170) REVERT: C 635 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7764 (t-90) REVERT: D 308 GLU cc_start: 0.8668 (tp30) cc_final: 0.8214 (mt-10) REVERT: D 312 GLN cc_start: 0.8920 (mt0) cc_final: 0.8626 (mt0) REVERT: D 327 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8798 (p) REVERT: D 412 MET cc_start: 0.8342 (mtp) cc_final: 0.7976 (mmp) REVERT: D 492 GLU cc_start: 0.8882 (tp30) cc_final: 0.8597 (tt0) REVERT: D 595 ILE cc_start: 0.8667 (mt) cc_final: 0.8373 (tp) REVERT: D 619 ASP cc_start: 0.8009 (m-30) cc_final: 0.7778 (t0) REVERT: E 132 HIS cc_start: 0.3301 (OUTLIER) cc_final: 0.2979 (t70) REVERT: E 314 ASP cc_start: 0.8664 (t0) cc_final: 0.8253 (t0) REVERT: E 492 GLU cc_start: 0.8689 (tp30) cc_final: 0.8332 (tt0) REVERT: E 501 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8391 (tm-30) REVERT: E 506 ASN cc_start: 0.8527 (t0) cc_final: 0.8183 (p0) REVERT: F 132 HIS cc_start: 0.3715 (OUTLIER) cc_final: 0.3331 (t70) REVERT: F 314 ASP cc_start: 0.8473 (t0) cc_final: 0.8238 (t0) REVERT: F 412 MET cc_start: 0.8001 (mtp) cc_final: 0.7766 (mmp) REVERT: F 445 ASN cc_start: 0.8681 (m-40) cc_final: 0.8273 (m110) REVERT: F 492 GLU cc_start: 0.8841 (tp30) cc_final: 0.8533 (tt0) REVERT: F 506 ASN cc_start: 0.8449 (t0) cc_final: 0.7870 (p0) REVERT: F 619 ASP cc_start: 0.8277 (m-30) cc_final: 0.8017 (t0) REVERT: G 312 GLN cc_start: 0.8943 (mt0) cc_final: 0.8703 (mt0) REVERT: G 314 ASP cc_start: 0.8565 (t0) cc_final: 0.8043 (t0) REVERT: G 412 MET cc_start: 0.8271 (mtp) cc_final: 0.7966 (mmp) REVERT: G 492 GLU cc_start: 0.8882 (tp30) cc_final: 0.8531 (tt0) REVERT: G 506 ASN cc_start: 0.8343 (t0) cc_final: 0.8085 (p0) REVERT: G 619 ASP cc_start: 0.8417 (m-30) cc_final: 0.8071 (t0) REVERT: H 312 GLN cc_start: 0.8890 (mt0) cc_final: 0.8665 (mt0) REVERT: H 314 ASP cc_start: 0.8427 (t0) cc_final: 0.8029 (t0) REVERT: H 412 MET cc_start: 0.7845 (mtp) cc_final: 0.7522 (mmt) REVERT: H 414 LEU cc_start: 0.8285 (mp) cc_final: 0.8082 (pp) REVERT: H 492 GLU cc_start: 0.8762 (tp30) cc_final: 0.8433 (tt0) REVERT: H 575 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8528 (ttmm) REVERT: H 618 MET cc_start: 0.8097 (mtp) cc_final: 0.7819 (mtp) REVERT: H 619 ASP cc_start: 0.8669 (m-30) cc_final: 0.8435 (t70) REVERT: I 132 HIS cc_start: 0.3069 (OUTLIER) cc_final: 0.2753 (t70) REVERT: I 241 ASN cc_start: 0.8090 (p0) cc_final: 0.7752 (m-40) REVERT: I 303 MET cc_start: 0.8091 (tpt) cc_final: 0.7824 (tpp) REVERT: I 314 ASP cc_start: 0.8559 (t0) cc_final: 0.8072 (t0) REVERT: I 412 MET cc_start: 0.8158 (mtp) cc_final: 0.7909 (mmp) REVERT: I 445 ASN cc_start: 0.8917 (m-40) cc_final: 0.8689 (m110) REVERT: I 492 GLU cc_start: 0.8829 (tp30) cc_final: 0.8581 (tt0) REVERT: I 620 ASP cc_start: 0.8447 (m-30) cc_final: 0.7748 (p0) REVERT: J 179 MET cc_start: 0.7663 (tpt) cc_final: 0.7442 (tpp) REVERT: J 289 GLN cc_start: 0.8439 (tp40) cc_final: 0.8203 (tm-30) REVERT: J 314 ASP cc_start: 0.8238 (t0) cc_final: 0.7942 (t0) REVERT: J 412 MET cc_start: 0.8315 (mtp) cc_final: 0.7891 (mmp) REVERT: J 445 ASN cc_start: 0.8394 (m-40) cc_final: 0.8078 (m110) REVERT: J 492 GLU cc_start: 0.8892 (tp30) cc_final: 0.8626 (tt0) REVERT: J 506 ASN cc_start: 0.8368 (t0) cc_final: 0.7484 (p0) REVERT: J 618 MET cc_start: 0.8217 (mtp) cc_final: 0.7897 (mtp) REVERT: J 619 ASP cc_start: 0.8562 (m-30) cc_final: 0.8333 (t0) REVERT: J 634 ARG cc_start: 0.8910 (ttm-80) cc_final: 0.8565 (ttp-170) REVERT: J 635 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7871 (t-90) REVERT: K 314 ASP cc_start: 0.8439 (t0) cc_final: 0.8053 (t0) REVERT: K 412 MET cc_start: 0.8131 (mtp) cc_final: 0.7858 (mmp) REVERT: K 492 GLU cc_start: 0.8837 (tp30) cc_final: 0.8536 (tt0) REVERT: K 619 ASP cc_start: 0.7887 (m-30) cc_final: 0.7621 (t70) REVERT: K 634 ARG cc_start: 0.8812 (ttm-80) cc_final: 0.8440 (ttp-170) REVERT: K 635 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7856 (t-90) REVERT: L 303 MET cc_start: 0.8254 (mmm) cc_final: 0.7983 (tpp) REVERT: L 314 ASP cc_start: 0.8580 (t0) cc_final: 0.8239 (t0) REVERT: L 412 MET cc_start: 0.7919 (mtp) cc_final: 0.7585 (mmt) REVERT: L 445 ASN cc_start: 0.8569 (m-40) cc_final: 0.8245 (m110) REVERT: L 492 GLU cc_start: 0.8706 (tp30) cc_final: 0.8421 (tt0) REVERT: L 546 LEU cc_start: 0.9286 (mp) cc_final: 0.8938 (tt) REVERT: L 619 ASP cc_start: 0.8184 (m-30) cc_final: 0.7890 (t0) REVERT: L 634 ARG cc_start: 0.8912 (ttm-80) cc_final: 0.8598 (ttp-170) REVERT: M 132 HIS cc_start: 0.2799 (OUTLIER) cc_final: 0.2334 (t70) REVERT: M 252 GLU cc_start: 0.8957 (tp30) cc_final: 0.8703 (pt0) REVERT: M 303 MET cc_start: 0.8477 (tpp) cc_final: 0.7892 (ttm) REVERT: M 307 GLN cc_start: 0.8524 (tp-100) cc_final: 0.7901 (mt0) REVERT: M 308 GLU cc_start: 0.8665 (tt0) cc_final: 0.8406 (tp30) REVERT: M 445 ASN cc_start: 0.8646 (m-40) cc_final: 0.8339 (m110) REVERT: M 506 ASN cc_start: 0.8427 (t0) cc_final: 0.8169 (p0) REVERT: M 533 GLN cc_start: 0.8549 (mt0) cc_final: 0.8271 (tt0) REVERT: M 573 GLU cc_start: 0.8961 (tt0) cc_final: 0.8678 (mt-10) REVERT: M 619 ASP cc_start: 0.8033 (m-30) cc_final: 0.7770 (t70) REVERT: N 412 MET cc_start: 0.8237 (mtp) cc_final: 0.7962 (mmp) REVERT: N 492 GLU cc_start: 0.8660 (tp30) cc_final: 0.8349 (tt0) REVERT: N 501 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8260 (tm-30) REVERT: N 506 ASN cc_start: 0.8551 (t0) cc_final: 0.8060 (p0) REVERT: N 575 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8442 (ttmm) REVERT: N 619 ASP cc_start: 0.8042 (m-30) cc_final: 0.7757 (t70) REVERT: O 327 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8681 (p) REVERT: O 412 MET cc_start: 0.8254 (mtp) cc_final: 0.7897 (mmp) REVERT: O 492 GLU cc_start: 0.8744 (tp30) cc_final: 0.8391 (tt0) REVERT: O 573 GLU cc_start: 0.8844 (tt0) cc_final: 0.8601 (mt-10) REVERT: O 619 ASP cc_start: 0.8070 (m-30) cc_final: 0.7782 (t70) outliers start: 215 outliers final: 152 residues processed: 931 average time/residue: 0.4851 time to fit residues: 791.3959 Evaluate side-chains 849 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 687 time to evaluate : 4.696 ------------------------------------------------------------------------------- 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 480 VAL 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 204 VAL 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 415 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 444 ASP 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 C residue 158 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 529 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 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 451 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 LEU 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 309 VAL 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 503 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 536 VAL 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 265 LEU 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 529 VAL Chi-restraints excluded: chain F residue 536 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 204 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 254 LEU 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 449 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 603 ILE 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 323 GLU Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 415 VAL Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 595 ILE Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 132 HIS 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 439 SER Chi-restraints excluded: chain I residue 443 MET Chi-restraints excluded: chain I residue 479 GLU 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 291 THR 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 564 LEU Chi-restraints excluded: chain J residue 635 HIS Chi-restraints excluded: chain J residue 643 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 254 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 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 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 514 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 537 LEU Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 204 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 546 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 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 451 ILE Chi-restraints excluded: chain N residue 454 GLU Chi-restraints excluded: chain N residue 534 MET 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 327 VAL Chi-restraints excluded: chain O residue 415 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 SER 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: 8.9990 chunk 282 optimal weight: 3.9990 chunk 423 optimal weight: 0.2980 chunk 213 optimal weight: 0.0570 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 450 optimal weight: 0.1980 chunk 482 optimal weight: 7.9990 chunk 350 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 556 optimal weight: 0.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN B 340 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 ASN ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN J 524 ASN L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 635 HIS ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 57015 Z= 0.199 Angle : 0.580 11.721 77175 Z= 0.295 Chirality : 0.046 0.202 9420 Planarity : 0.005 0.089 10065 Dihedral : 4.466 21.646 7875 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.73 % Rotamer: Outliers : 3.03 % Allowed : 19.95 % Favored : 77.02 % 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: -2.14 (0.10), residues: 7290 helix: 0.56 (0.11), residues: 2265 sheet: -2.47 (0.09), residues: 2655 loop : -1.80 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 341 HIS 0.005 0.001 HIS K 635 PHE 0.007 0.001 PHE D 450 TYR 0.019 0.001 TYR A 352 ARG 0.012 0.000 ARG B 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 947 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 759 time to evaluate : 4.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8557 (t0) cc_final: 0.8130 (t0) REVERT: A 412 MET cc_start: 0.8013 (mtp) cc_final: 0.7800 (mmt) REVERT: A 445 ASN cc_start: 0.8343 (m-40) cc_final: 0.7973 (m110) REVERT: A 492 GLU cc_start: 0.8769 (tp30) cc_final: 0.8423 (tt0) REVERT: A 506 ASN cc_start: 0.8633 (t0) cc_final: 0.8277 (p0) REVERT: A 619 ASP cc_start: 0.8280 (m-30) cc_final: 0.8007 (t70) REVERT: A 620 ASP cc_start: 0.8288 (m-30) cc_final: 0.7479 (p0) REVERT: B 132 HIS cc_start: 0.2824 (OUTLIER) cc_final: 0.2514 (t70) REVERT: B 308 GLU cc_start: 0.8581 (tp30) cc_final: 0.8335 (mt-10) REVERT: B 312 GLN cc_start: 0.8581 (mt0) cc_final: 0.8341 (mt0) REVERT: B 412 MET cc_start: 0.7975 (mtp) cc_final: 0.7653 (mmp) REVERT: B 445 ASN cc_start: 0.8707 (m-40) cc_final: 0.8442 (m110) REVERT: B 492 GLU cc_start: 0.8856 (tp30) cc_final: 0.8574 (tt0) REVERT: B 501 GLU cc_start: 0.8477 (mp0) cc_final: 0.8185 (tm-30) REVERT: B 524 ASN cc_start: 0.8700 (p0) cc_final: 0.8364 (p0) REVERT: B 619 ASP cc_start: 0.7915 (m-30) cc_final: 0.7480 (t70) REVERT: B 622 HIS cc_start: 0.8769 (m170) cc_final: 0.8547 (m-70) REVERT: C 412 MET cc_start: 0.8446 (mtp) cc_final: 0.7962 (mmp) REVERT: C 492 GLU cc_start: 0.8902 (tp30) cc_final: 0.8598 (tt0) REVERT: C 501 GLU cc_start: 0.8545 (mp0) cc_final: 0.8173 (tm-30) REVERT: C 506 ASN cc_start: 0.8407 (t0) cc_final: 0.7918 (p0) REVERT: C 522 GLN cc_start: 0.8783 (tt0) cc_final: 0.8515 (tt0) REVERT: C 546 LEU cc_start: 0.9421 (mp) cc_final: 0.9070 (tt) REVERT: C 619 ASP cc_start: 0.8514 (m-30) cc_final: 0.8251 (t70) REVERT: C 634 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8525 (ttp-170) REVERT: C 635 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7629 (t-90) REVERT: D 308 GLU cc_start: 0.8617 (tp30) cc_final: 0.8310 (mt-10) REVERT: D 327 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8738 (p) REVERT: D 412 MET cc_start: 0.8264 (mtp) cc_final: 0.7931 (mmp) REVERT: D 492 GLU cc_start: 0.8818 (tp30) cc_final: 0.8531 (tt0) REVERT: D 595 ILE cc_start: 0.8638 (mt) cc_final: 0.8354 (tp) REVERT: D 619 ASP cc_start: 0.7909 (m-30) cc_final: 0.7675 (t70) REVERT: E 132 HIS cc_start: 0.3277 (OUTLIER) cc_final: 0.2904 (t70) REVERT: E 314 ASP cc_start: 0.8622 (t0) cc_final: 0.7955 (t0) REVERT: E 492 GLU cc_start: 0.8693 (tp30) cc_final: 0.8341 (tt0) REVERT: E 501 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8359 (tm-30) REVERT: E 506 ASN cc_start: 0.8470 (t0) cc_final: 0.8066 (p0) REVERT: F 132 HIS cc_start: 0.3683 (OUTLIER) cc_final: 0.3199 (t70) REVERT: F 312 GLN cc_start: 0.8924 (mt0) cc_final: 0.8575 (pt0) REVERT: F 314 ASP cc_start: 0.8409 (t0) cc_final: 0.8174 (t0) REVERT: F 412 MET cc_start: 0.7926 (mtp) cc_final: 0.7682 (mmp) REVERT: F 492 GLU cc_start: 0.8769 (tp30) cc_final: 0.8447 (tt0) REVERT: F 506 ASN cc_start: 0.8405 (t0) cc_final: 0.8062 (p0) REVERT: F 619 ASP cc_start: 0.8084 (m-30) cc_final: 0.7839 (t0) REVERT: G 314 ASP cc_start: 0.8506 (t0) cc_final: 0.7944 (t0) REVERT: G 412 MET cc_start: 0.8303 (mtp) cc_final: 0.7816 (mmp) REVERT: G 414 LEU cc_start: 0.8091 (mm) cc_final: 0.7830 (pp) REVERT: G 492 GLU cc_start: 0.8810 (tp30) cc_final: 0.8500 (tt0) REVERT: G 501 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7817 (mp0) REVERT: G 619 ASP cc_start: 0.8329 (m-30) cc_final: 0.7983 (t70) REVERT: H 314 ASP cc_start: 0.8354 (t0) cc_final: 0.7712 (t0) REVERT: H 397 TYR cc_start: 0.8036 (m-80) cc_final: 0.7773 (m-80) REVERT: H 412 MET cc_start: 0.7789 (mtp) cc_final: 0.7542 (mmt) REVERT: H 492 GLU cc_start: 0.8718 (tp30) cc_final: 0.8398 (tt0) REVERT: H 506 ASN cc_start: 0.8492 (t0) cc_final: 0.7772 (p0) REVERT: H 522 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8721 (tt0) REVERT: H 575 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8445 (ttmm) REVERT: H 618 MET cc_start: 0.8037 (mtp) cc_final: 0.7760 (mtp) REVERT: H 619 ASP cc_start: 0.8535 (m-30) cc_final: 0.8258 (t70) REVERT: I 241 ASN cc_start: 0.8066 (p0) cc_final: 0.7741 (m-40) REVERT: I 303 MET cc_start: 0.8080 (tpt) cc_final: 0.7803 (tpp) REVERT: I 412 MET cc_start: 0.8138 (mtp) cc_final: 0.7812 (mmp) REVERT: I 492 GLU cc_start: 0.8801 (tp30) cc_final: 0.8499 (tt0) REVERT: I 506 ASN cc_start: 0.8441 (t0) cc_final: 0.7829 (p0) REVERT: I 620 ASP cc_start: 0.8437 (m-30) cc_final: 0.7740 (p0) REVERT: J 412 MET cc_start: 0.8311 (mtp) cc_final: 0.7890 (mmp) REVERT: J 492 GLU cc_start: 0.8812 (tp30) cc_final: 0.8535 (tt0) REVERT: J 506 ASN cc_start: 0.8370 (t0) cc_final: 0.7724 (p0) REVERT: J 618 MET cc_start: 0.8168 (mtp) cc_final: 0.7831 (mtp) REVERT: J 619 ASP cc_start: 0.8489 (m-30) cc_final: 0.8246 (t0) REVERT: J 634 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8557 (ttp-170) REVERT: J 635 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7880 (t-90) REVERT: K 312 GLN cc_start: 0.8770 (mt0) cc_final: 0.8340 (pt0) REVERT: K 314 ASP cc_start: 0.8377 (t0) cc_final: 0.7972 (t0) REVERT: K 412 MET cc_start: 0.8079 (mtp) cc_final: 0.7807 (mmp) REVERT: K 414 LEU cc_start: 0.8242 (mm) cc_final: 0.7929 (pp) REVERT: K 492 GLU cc_start: 0.8805 (tp30) cc_final: 0.8512 (tt0) REVERT: K 506 ASN cc_start: 0.8434 (t0) cc_final: 0.7956 (p0) REVERT: K 619 ASP cc_start: 0.7891 (m-30) cc_final: 0.7674 (t70) REVERT: K 634 ARG cc_start: 0.8787 (ttm-80) cc_final: 0.8439 (ttp-170) REVERT: K 635 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7822 (t-90) REVERT: L 303 MET cc_start: 0.8222 (mmm) cc_final: 0.7940 (tpp) REVERT: L 314 ASP cc_start: 0.8528 (t0) cc_final: 0.8190 (t0) REVERT: L 412 MET cc_start: 0.7865 (mtp) cc_final: 0.7513 (mmt) REVERT: L 445 ASN cc_start: 0.8493 (m-40) cc_final: 0.8193 (m110) REVERT: L 492 GLU cc_start: 0.8671 (tp30) cc_final: 0.8366 (tt0) REVERT: L 506 ASN cc_start: 0.8467 (t0) cc_final: 0.7825 (p0) REVERT: L 546 LEU cc_start: 0.9270 (mp) cc_final: 0.8932 (tt) REVERT: L 619 ASP cc_start: 0.8135 (m-30) cc_final: 0.7847 (t70) REVERT: L 634 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8484 (ttp-170) REVERT: M 132 HIS cc_start: 0.2872 (OUTLIER) cc_final: 0.2381 (t70) REVERT: M 252 GLU cc_start: 0.8947 (tp30) cc_final: 0.8706 (pt0) REVERT: M 303 MET cc_start: 0.8451 (tpp) cc_final: 0.7913 (ttm) REVERT: M 307 GLN cc_start: 0.8465 (tp-100) cc_final: 0.7919 (mt0) REVERT: M 308 GLU cc_start: 0.8677 (tt0) cc_final: 0.8430 (tp30) REVERT: M 533 GLN cc_start: 0.8549 (mt0) cc_final: 0.8301 (tt0) REVERT: M 573 GLU cc_start: 0.8913 (tt0) cc_final: 0.8630 (mt-10) REVERT: M 619 ASP cc_start: 0.8021 (m-30) cc_final: 0.7727 (t70) REVERT: N 303 MET cc_start: 0.8256 (tpp) cc_final: 0.8054 (mpp) REVERT: N 412 MET cc_start: 0.8183 (mtp) cc_final: 0.7895 (mmp) REVERT: N 492 GLU cc_start: 0.8629 (tp30) cc_final: 0.8324 (tt0) REVERT: N 501 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8192 (tm-30) REVERT: N 506 ASN cc_start: 0.8490 (t0) cc_final: 0.8131 (p0) REVERT: N 575 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8491 (ttmm) REVERT: N 595 ILE cc_start: 0.8727 (mt) cc_final: 0.8350 (tp) REVERT: N 609 TYR cc_start: 0.8583 (t80) cc_final: 0.8381 (t80) REVERT: N 619 ASP cc_start: 0.7780 (m-30) cc_final: 0.7524 (t70) REVERT: O 327 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8633 (p) REVERT: O 412 MET cc_start: 0.8343 (mtp) cc_final: 0.7976 (mmp) REVERT: O 492 GLU cc_start: 0.8687 (tp30) cc_final: 0.8368 (tt0) REVERT: O 506 ASN cc_start: 0.8344 (t0) cc_final: 0.8087 (p0) REVERT: O 573 GLU cc_start: 0.8848 (tt0) cc_final: 0.8611 (mt-10) REVERT: O 619 ASP cc_start: 0.8019 (m-30) cc_final: 0.7717 (t70) outliers start: 188 outliers final: 128 residues processed: 915 average time/residue: 0.4989 time to fit residues: 796.7423 Evaluate side-chains 806 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 668 time to evaluate : 4.805 ------------------------------------------------------------------------------- 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 426 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 VAL 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 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 451 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 503 GLU 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 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 451 ILE Chi-restraints excluded: chain C residue 529 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 327 VAL Chi-restraints excluded: chain D residue 426 VAL 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 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 449 SER Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain F residue 132 HIS Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 265 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 536 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 327 VAL Chi-restraints excluded: chain G residue 363 MET 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 603 ILE 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 415 VAL Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 595 ILE Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 246 LEU 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 603 ILE Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 327 VAL 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 603 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 327 VAL Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 635 HIS Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 514 VAL 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 635 HIS Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 204 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 546 LEU 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 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 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 291 THR 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 603 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 8.9990 chunk 678 optimal weight: 5.9990 chunk 619 optimal weight: 0.8980 chunk 660 optimal weight: 0.9980 chunk 397 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 518 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 596 optimal weight: 6.9990 chunk 624 optimal weight: 0.9990 chunk 657 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 ASN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 506 ASN ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 408 ASN L 408 ASN L 489 GLN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 635 HIS ** M 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 445 ASN N 489 GLN ** 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: 0.7908 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 57015 Z= 0.332 Angle : 0.640 13.499 77175 Z= 0.324 Chirality : 0.047 0.223 9420 Planarity : 0.006 0.087 10065 Dihedral : 4.680 22.488 7875 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.97 % Favored : 91.82 % Rotamer: Outliers : 3.27 % Allowed : 20.29 % Favored : 76.44 % 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: -2.11 (0.10), residues: 7290 helix: 0.52 (0.11), residues: 2265 sheet: -2.50 (0.10), residues: 2640 loop : -1.66 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 341 HIS 0.008 0.001 HIS L 635 PHE 0.007 0.002 PHE G 518 TYR 0.024 0.002 TYR F 609 ARG 0.011 0.001 ARG C 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 899 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 696 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8611 (t0) cc_final: 0.8214 (t0) REVERT: A 412 MET cc_start: 0.8040 (mtp) cc_final: 0.7750 (mmt) REVERT: A 445 ASN cc_start: 0.8585 (m-40) cc_final: 0.8213 (m110) REVERT: A 492 GLU cc_start: 0.8884 (tp30) cc_final: 0.8568 (tt0) REVERT: A 506 ASN cc_start: 0.8729 (t0) cc_final: 0.8325 (p0) REVERT: A 619 ASP cc_start: 0.8270 (m-30) cc_final: 0.7995 (t70) REVERT: A 620 ASP cc_start: 0.8491 (m-30) cc_final: 0.7712 (p0) REVERT: B 132 HIS cc_start: 0.3078 (OUTLIER) cc_final: 0.2726 (t70) REVERT: B 308 GLU cc_start: 0.8598 (tp30) cc_final: 0.8377 (mt-10) REVERT: B 312 GLN cc_start: 0.8700 (mt0) cc_final: 0.8425 (mt0) REVERT: B 412 MET cc_start: 0.8096 (mtp) cc_final: 0.7793 (mmp) REVERT: B 445 ASN cc_start: 0.8794 (m-40) cc_final: 0.8549 (m110) REVERT: B 492 GLU cc_start: 0.8878 (tp30) cc_final: 0.8592 (tt0) REVERT: B 619 ASP cc_start: 0.8008 (m-30) cc_final: 0.7700 (t70) REVERT: C 412 MET cc_start: 0.8428 (mtp) cc_final: 0.8045 (mmp) REVERT: C 492 GLU cc_start: 0.8911 (tp30) cc_final: 0.8598 (tt0) REVERT: C 501 GLU cc_start: 0.8630 (mp0) cc_final: 0.8275 (tm-30) REVERT: C 506 ASN cc_start: 0.8527 (t0) cc_final: 0.7684 (p0) REVERT: C 546 LEU cc_start: 0.9419 (mp) cc_final: 0.9076 (tp) REVERT: C 590 MET cc_start: 0.8273 (ttm) cc_final: 0.7976 (tmm) REVERT: C 619 ASP cc_start: 0.8528 (m-30) cc_final: 0.8262 (t70) REVERT: C 634 ARG cc_start: 0.8882 (ttm-80) cc_final: 0.8607 (ttp-170) REVERT: C 635 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7831 (t-90) REVERT: D 327 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8814 (p) REVERT: D 412 MET cc_start: 0.8228 (mtp) cc_final: 0.7891 (mmp) REVERT: D 492 GLU cc_start: 0.8902 (tp30) cc_final: 0.8624 (tt0) REVERT: D 595 ILE cc_start: 0.8698 (mt) cc_final: 0.8399 (tp) REVERT: D 619 ASP cc_start: 0.8066 (m-30) cc_final: 0.7843 (t70) REVERT: E 132 HIS cc_start: 0.3357 (OUTLIER) cc_final: 0.3021 (t70) REVERT: E 314 ASP cc_start: 0.8684 (t0) cc_final: 0.8240 (t0) REVERT: E 492 GLU cc_start: 0.8759 (tp30) cc_final: 0.8408 (tt0) REVERT: E 501 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8491 (tm-30) REVERT: E 506 ASN cc_start: 0.8581 (t0) cc_final: 0.8261 (p0) REVERT: F 314 ASP cc_start: 0.8454 (t0) cc_final: 0.7973 (t0) REVERT: F 485 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8385 (ttpp) REVERT: F 492 GLU cc_start: 0.8854 (tp30) cc_final: 0.8527 (tt0) REVERT: F 501 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7743 (mp0) REVERT: F 506 ASN cc_start: 0.8515 (t0) cc_final: 0.8134 (p0) REVERT: F 619 ASP cc_start: 0.8339 (m-30) cc_final: 0.8085 (t0) REVERT: G 314 ASP cc_start: 0.8621 (t0) cc_final: 0.8080 (t0) REVERT: G 412 MET cc_start: 0.8221 (mtp) cc_final: 0.7893 (mmp) REVERT: G 492 GLU cc_start: 0.8922 (tp30) cc_final: 0.8595 (tt0) REVERT: G 619 ASP cc_start: 0.8424 (m-30) cc_final: 0.8092 (t70) REVERT: H 314 ASP cc_start: 0.8438 (t0) cc_final: 0.8027 (t0) REVERT: H 412 MET cc_start: 0.7903 (mtp) cc_final: 0.7609 (mmt) REVERT: H 492 GLU cc_start: 0.8764 (tp30) cc_final: 0.8445 (tt0) REVERT: H 575 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8503 (ttmm) REVERT: H 618 MET cc_start: 0.8219 (mtp) cc_final: 0.7952 (mtp) REVERT: H 619 ASP cc_start: 0.8744 (m-30) cc_final: 0.8488 (t70) REVERT: I 132 HIS cc_start: 0.3185 (OUTLIER) cc_final: 0.2842 (t70) REVERT: I 303 MET cc_start: 0.8165 (tpt) cc_final: 0.7931 (tpp) REVERT: I 314 ASP cc_start: 0.8418 (t0) cc_final: 0.7899 (t0) REVERT: I 412 MET cc_start: 0.8188 (mtp) cc_final: 0.7881 (mmp) REVERT: I 492 GLU cc_start: 0.8894 (tp30) cc_final: 0.8596 (tt0) REVERT: I 575 LYS cc_start: 0.8611 (ttpt) cc_final: 0.8369 (ttmm) REVERT: I 620 ASP cc_start: 0.8579 (m-30) cc_final: 0.7934 (p0) REVERT: J 179 MET cc_start: 0.7648 (tpt) cc_final: 0.7408 (tpp) REVERT: J 203 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7812 (tp) REVERT: J 314 ASP cc_start: 0.8229 (t0) cc_final: 0.7964 (t0) REVERT: J 412 MET cc_start: 0.8369 (mtp) cc_final: 0.8022 (mmp) REVERT: J 492 GLU cc_start: 0.8897 (tp30) cc_final: 0.8627 (tt0) REVERT: J 618 MET cc_start: 0.8273 (mtp) cc_final: 0.7955 (mtp) REVERT: J 619 ASP cc_start: 0.8592 (m-30) cc_final: 0.8376 (t0) REVERT: J 634 ARG cc_start: 0.8944 (ttm-80) cc_final: 0.8629 (ttp-170) REVERT: J 635 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7908 (t-90) REVERT: K 307 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8548 (mm-40) REVERT: K 314 ASP cc_start: 0.8483 (t0) cc_final: 0.8067 (t0) REVERT: K 412 MET cc_start: 0.8062 (mtp) cc_final: 0.7816 (mmp) REVERT: K 492 GLU cc_start: 0.8855 (tp30) cc_final: 0.8557 (tt0) REVERT: K 619 ASP cc_start: 0.7943 (m-30) cc_final: 0.7660 (t70) REVERT: K 634 ARG cc_start: 0.8799 (ttm-80) cc_final: 0.8454 (ttp-170) REVERT: K 635 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7814 (t-90) REVERT: L 303 MET cc_start: 0.8281 (mmm) cc_final: 0.8020 (tpp) REVERT: L 314 ASP cc_start: 0.8592 (t0) cc_final: 0.8286 (t0) REVERT: L 412 MET cc_start: 0.7957 (mtp) cc_final: 0.7564 (mmp) REVERT: L 445 ASN cc_start: 0.8635 (m-40) cc_final: 0.8316 (m110) REVERT: L 492 GLU cc_start: 0.8779 (tp30) cc_final: 0.8478 (tt0) REVERT: L 546 LEU cc_start: 0.9262 (mp) cc_final: 0.8919 (tt) REVERT: L 619 ASP cc_start: 0.8173 (m-30) cc_final: 0.7875 (t0) REVERT: L 634 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8446 (ttp-170) REVERT: L 635 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7413 (t70) REVERT: M 252 GLU cc_start: 0.9017 (tp30) cc_final: 0.8742 (pt0) REVERT: M 303 MET cc_start: 0.8451 (tpp) cc_final: 0.8120 (tpp) REVERT: M 307 GLN cc_start: 0.8557 (tp-100) cc_final: 0.7922 (mt0) REVERT: M 308 GLU cc_start: 0.8681 (tt0) cc_final: 0.8427 (tp30) REVERT: M 533 GLN cc_start: 0.8525 (mt0) cc_final: 0.8281 (tt0) REVERT: M 573 GLU cc_start: 0.8944 (tt0) cc_final: 0.8664 (mt-10) REVERT: M 619 ASP cc_start: 0.8120 (m-30) cc_final: 0.7874 (t70) REVERT: N 412 MET cc_start: 0.8253 (mtp) cc_final: 0.7848 (mmp) REVERT: N 492 GLU cc_start: 0.8916 (tp30) cc_final: 0.8627 (tt0) REVERT: N 501 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8375 (tm-30) REVERT: N 506 ASN cc_start: 0.8558 (t0) cc_final: 0.8072 (p0) REVERT: N 575 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8430 (ttmm) REVERT: N 619 ASP cc_start: 0.7857 (m-30) cc_final: 0.7613 (t70) REVERT: O 314 ASP cc_start: 0.8248 (t0) cc_final: 0.7768 (t0) REVERT: O 327 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8660 (p) REVERT: O 412 MET cc_start: 0.8304 (mtp) cc_final: 0.7958 (mmp) REVERT: O 492 GLU cc_start: 0.8732 (tp30) cc_final: 0.8411 (tt0) REVERT: O 573 GLU cc_start: 0.8829 (tt0) cc_final: 0.8584 (mt-10) REVERT: O 619 ASP cc_start: 0.8126 (m-30) cc_final: 0.7828 (t70) outliers start: 203 outliers final: 161 residues processed: 863 average time/residue: 0.4893 time to fit residues: 742.1217 Evaluate side-chains 834 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 663 time to evaluate : 4.772 ------------------------------------------------------------------------------- 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 449 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 VAL 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 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 444 ASP Chi-restraints excluded: chain B residue 451 ILE 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 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 404 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 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 327 VAL Chi-restraints excluded: chain D residue 426 VAL 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 603 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 309 VAL 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 503 GLU 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 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 536 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 204 VAL 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 449 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 323 GLU 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 439 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 595 ILE Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain H residue 635 HIS Chi-restraints excluded: chain I residue 132 HIS 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 345 GLU 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 439 SER 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 203 LEU Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 363 MET 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 564 LEU 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 204 VAL Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 635 HIS Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 291 THR 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 536 VAL Chi-restraints excluded: chain L residue 537 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 L residue 635 HIS Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 204 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 480 VAL Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 546 LEU 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 414 LEU 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 454 GLU Chi-restraints excluded: chain N residue 534 MET Chi-restraints excluded: chain N residue 554 LEU 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 291 THR 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 439 SER Chi-restraints excluded: chain O residue 449 SER Chi-restraints excluded: chain O residue 595 ILE Chi-restraints excluded: chain O residue 603 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 5.9990 chunk 698 optimal weight: 0.0010 chunk 426 optimal weight: 0.0370 chunk 331 optimal weight: 1.9990 chunk 485 optimal weight: 3.9990 chunk 732 optimal weight: 3.9990 chunk 673 optimal weight: 0.5980 chunk 583 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 450 optimal weight: 0.0980 chunk 357 optimal weight: 2.9990 overall best weight: 0.5466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 522 GLN ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 GLN L 445 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 489 GLN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 57015 Z= 0.199 Angle : 0.591 14.284 77175 Z= 0.299 Chirality : 0.046 0.260 9420 Planarity : 0.005 0.085 10065 Dihedral : 4.428 22.311 7875 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.86 % Favored : 94.94 % Rotamer: Outliers : 2.45 % Allowed : 21.19 % Favored : 76.36 % 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: -1.96 (0.10), residues: 7290 helix: 0.72 (0.11), residues: 2250 sheet: -2.43 (0.10), residues: 2655 loop : -1.60 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 341 HIS 0.007 0.001 HIS L 635 PHE 0.010 0.001 PHE L 642 TYR 0.021 0.001 TYR N 609 ARG 0.015 0.000 ARG L 634 ********************** 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 867 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 715 time to evaluate : 4.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8531 (t0) cc_final: 0.8090 (t0) REVERT: A 412 MET cc_start: 0.8002 (mtp) cc_final: 0.7724 (mmt) REVERT: A 445 ASN cc_start: 0.8333 (m-40) cc_final: 0.7912 (m110) REVERT: A 492 GLU cc_start: 0.8822 (tp30) cc_final: 0.8505 (tt0) REVERT: A 506 ASN cc_start: 0.8618 (t0) cc_final: 0.8263 (p0) REVERT: A 619 ASP cc_start: 0.8094 (m-30) cc_final: 0.7782 (t70) REVERT: A 620 ASP cc_start: 0.8335 (m-30) cc_final: 0.7580 (p0) REVERT: B 132 HIS cc_start: 0.2957 (OUTLIER) cc_final: 0.2613 (t70) REVERT: B 308 GLU cc_start: 0.8609 (tp30) cc_final: 0.8367 (mt-10) REVERT: B 312 GLN cc_start: 0.8598 (mt0) cc_final: 0.8348 (mt0) REVERT: B 412 MET cc_start: 0.8076 (mtp) cc_final: 0.7754 (mmp) REVERT: B 445 ASN cc_start: 0.8655 (m-40) cc_final: 0.8396 (m110) REVERT: B 492 GLU cc_start: 0.8801 (tp30) cc_final: 0.8504 (tt0) REVERT: B 501 GLU cc_start: 0.8441 (mp0) cc_final: 0.8190 (tm-30) REVERT: B 524 ASN cc_start: 0.8704 (p0) cc_final: 0.8391 (p0) REVERT: B 619 ASP cc_start: 0.7919 (m-30) cc_final: 0.7603 (t70) REVERT: C 303 MET cc_start: 0.8208 (mmm) cc_final: 0.7551 (mtm) REVERT: C 314 ASP cc_start: 0.8140 (t0) cc_final: 0.7858 (t0) REVERT: C 412 MET cc_start: 0.8392 (mtp) cc_final: 0.8075 (mmp) REVERT: C 492 GLU cc_start: 0.8894 (tp30) cc_final: 0.8596 (tt0) REVERT: C 501 GLU cc_start: 0.8543 (mp0) cc_final: 0.8178 (tm-30) REVERT: C 506 ASN cc_start: 0.8496 (t0) cc_final: 0.8034 (p0) REVERT: C 522 GLN cc_start: 0.8790 (tt0) cc_final: 0.8433 (tt0) REVERT: C 546 LEU cc_start: 0.9420 (mp) cc_final: 0.9058 (tt) REVERT: C 619 ASP cc_start: 0.8411 (m-30) cc_final: 0.8135 (t70) REVERT: C 633 LYS cc_start: 0.7391 (tppt) cc_final: 0.7156 (tptt) REVERT: C 634 ARG cc_start: 0.8778 (ttm-80) cc_final: 0.8372 (ttp-170) REVERT: C 635 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7634 (t-90) REVERT: D 412 MET cc_start: 0.8254 (mtp) cc_final: 0.7926 (mmp) REVERT: D 492 GLU cc_start: 0.8840 (tp30) cc_final: 0.8557 (tt0) REVERT: D 595 ILE cc_start: 0.8657 (mt) cc_final: 0.8356 (tp) REVERT: D 609 TYR cc_start: 0.8642 (t80) cc_final: 0.8439 (t80) REVERT: D 619 ASP cc_start: 0.7896 (m-30) cc_final: 0.7667 (t70) REVERT: E 132 HIS cc_start: 0.3197 (OUTLIER) cc_final: 0.2868 (t70) REVERT: E 314 ASP cc_start: 0.8575 (t0) cc_final: 0.7872 (t0) REVERT: E 492 GLU cc_start: 0.8713 (tp30) cc_final: 0.8360 (tt0) REVERT: E 501 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8249 (tm-30) REVERT: E 506 ASN cc_start: 0.8446 (t0) cc_final: 0.8009 (p0) REVERT: E 547 GLU cc_start: 0.8385 (tt0) cc_final: 0.8067 (tm-30) REVERT: E 595 ILE cc_start: 0.8804 (mt) cc_final: 0.8591 (tp) REVERT: E 634 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8272 (ttp-170) REVERT: F 303 MET cc_start: 0.8197 (mmm) cc_final: 0.7523 (ttm) REVERT: F 314 ASP cc_start: 0.8407 (t0) cc_final: 0.8164 (t0) REVERT: F 492 GLU cc_start: 0.8791 (tp30) cc_final: 0.8481 (tt0) REVERT: F 506 ASN cc_start: 0.8444 (t0) cc_final: 0.8158 (p0) REVERT: F 546 LEU cc_start: 0.9366 (mp) cc_final: 0.9010 (tt) REVERT: F 619 ASP cc_start: 0.8166 (m-30) cc_final: 0.7914 (t0) REVERT: G 314 ASP cc_start: 0.8488 (t0) cc_final: 0.8172 (t0) REVERT: G 412 MET cc_start: 0.8125 (mtp) cc_final: 0.7808 (mmp) REVERT: G 492 GLU cc_start: 0.8820 (tp30) cc_final: 0.8518 (tt0) REVERT: G 501 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7801 (mp0) REVERT: G 619 ASP cc_start: 0.8261 (m-30) cc_final: 0.7949 (t70) REVERT: H 314 ASP cc_start: 0.8322 (t0) cc_final: 0.7704 (t0) REVERT: H 412 MET cc_start: 0.7931 (mtp) cc_final: 0.7613 (mmt) REVERT: H 492 GLU cc_start: 0.8671 (tp30) cc_final: 0.8366 (tt0) REVERT: H 506 ASN cc_start: 0.8497 (t0) cc_final: 0.7833 (p0) REVERT: H 522 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: H 618 MET cc_start: 0.8050 (mtp) cc_final: 0.7772 (mtp) REVERT: H 619 ASP cc_start: 0.8507 (m-30) cc_final: 0.8229 (t70) REVERT: I 303 MET cc_start: 0.8080 (tpt) cc_final: 0.7840 (tpp) REVERT: I 314 ASP cc_start: 0.8242 (t0) cc_final: 0.7841 (t0) REVERT: I 412 MET cc_start: 0.8066 (mtp) cc_final: 0.7781 (mmp) REVERT: I 492 GLU cc_start: 0.8825 (tp30) cc_final: 0.8524 (tt0) REVERT: I 506 ASN cc_start: 0.8326 (t0) cc_final: 0.7683 (p0) REVERT: I 575 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8345 (ttmm) REVERT: I 620 ASP cc_start: 0.8381 (m-30) cc_final: 0.7791 (p0) REVERT: J 179 MET cc_start: 0.7694 (tpt) cc_final: 0.7436 (tpp) REVERT: J 203 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7619 (tp) REVERT: J 312 GLN cc_start: 0.8758 (mt0) cc_final: 0.8506 (pt0) REVERT: J 412 MET cc_start: 0.8395 (mtp) cc_final: 0.8036 (mmp) REVERT: J 492 GLU cc_start: 0.8830 (tp30) cc_final: 0.8566 (tt0) REVERT: J 506 ASN cc_start: 0.8413 (t0) cc_final: 0.7803 (p0) REVERT: J 619 ASP cc_start: 0.8508 (m-30) cc_final: 0.8282 (t0) REVERT: J 634 ARG cc_start: 0.8931 (ttm-80) cc_final: 0.8648 (ttp-170) REVERT: J 635 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7887 (t-90) REVERT: K 303 MET cc_start: 0.7915 (mmm) cc_final: 0.7156 (ttm) REVERT: K 312 GLN cc_start: 0.8836 (mt0) cc_final: 0.8390 (pt0) REVERT: K 314 ASP cc_start: 0.8354 (t0) cc_final: 0.7688 (t0) REVERT: K 412 MET cc_start: 0.8105 (mtp) cc_final: 0.7854 (mmp) REVERT: K 414 LEU cc_start: 0.8233 (mm) cc_final: 0.7968 (pp) REVERT: K 492 GLU cc_start: 0.8763 (tp30) cc_final: 0.8475 (tt0) REVERT: K 506 ASN cc_start: 0.8399 (t0) cc_final: 0.7902 (p0) REVERT: K 595 ILE cc_start: 0.8668 (mt) cc_final: 0.8426 (tp) REVERT: K 619 ASP cc_start: 0.7886 (m-30) cc_final: 0.7664 (t70) REVERT: K 634 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8406 (ttp-170) REVERT: K 635 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7738 (t-90) REVERT: L 303 MET cc_start: 0.8219 (mmm) cc_final: 0.7962 (tpp) REVERT: L 314 ASP cc_start: 0.8395 (t0) cc_final: 0.8050 (t0) REVERT: L 412 MET cc_start: 0.7936 (mtp) cc_final: 0.7550 (mmp) REVERT: L 492 GLU cc_start: 0.8691 (tp30) cc_final: 0.8380 (tt0) REVERT: L 506 ASN cc_start: 0.8355 (t0) cc_final: 0.7694 (p0) REVERT: L 546 LEU cc_start: 0.9272 (mp) cc_final: 0.8920 (tt) REVERT: L 619 ASP cc_start: 0.8097 (m-30) cc_final: 0.7816 (t70) REVERT: M 252 GLU cc_start: 0.8822 (tp30) cc_final: 0.8598 (pt0) REVERT: M 303 MET cc_start: 0.8440 (tpp) cc_final: 0.8133 (tpp) REVERT: M 307 GLN cc_start: 0.8440 (tp-100) cc_final: 0.7910 (mt0) REVERT: M 308 GLU cc_start: 0.8663 (tt0) cc_final: 0.8437 (tp30) REVERT: M 314 ASP cc_start: 0.8285 (t0) cc_final: 0.8040 (t0) REVERT: M 533 GLN cc_start: 0.8509 (mt0) cc_final: 0.8271 (tt0) REVERT: M 619 ASP cc_start: 0.7974 (m-30) cc_final: 0.7728 (t70) REVERT: N 412 MET cc_start: 0.8174 (mtp) cc_final: 0.7789 (mmp) REVERT: N 414 LEU cc_start: 0.8024 (mm) cc_final: 0.7705 (pp) REVERT: N 444 ASP cc_start: 0.8214 (m-30) cc_final: 0.8001 (t0) REVERT: N 492 GLU cc_start: 0.8692 (tp30) cc_final: 0.8373 (tt0) REVERT: N 501 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8145 (tm-30) REVERT: N 506 ASN cc_start: 0.8444 (t0) cc_final: 0.8117 (p0) REVERT: N 575 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8475 (ttmm) REVERT: N 595 ILE cc_start: 0.8728 (mt) cc_final: 0.8347 (tp) REVERT: N 619 ASP cc_start: 0.7664 (m-30) cc_final: 0.7394 (t70) REVERT: O 327 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8549 (p) REVERT: O 412 MET cc_start: 0.8356 (mtp) cc_final: 0.8000 (mmp) REVERT: O 414 LEU cc_start: 0.8228 (mm) cc_final: 0.8024 (pp) REVERT: O 492 GLU cc_start: 0.8736 (tp30) cc_final: 0.8431 (tt0) REVERT: O 506 ASN cc_start: 0.8355 (t0) cc_final: 0.8009 (p0) REVERT: O 573 GLU cc_start: 0.8660 (tt0) cc_final: 0.8405 (mt-10) REVERT: O 619 ASP cc_start: 0.7992 (m-30) cc_final: 0.7687 (t70) outliers start: 152 outliers final: 125 residues processed: 845 average time/residue: 0.5088 time to fit residues: 752.9670 Evaluate side-chains 808 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 675 time to evaluate : 4.682 ------------------------------------------------------------------------------- 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 426 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 554 LEU 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 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 444 ASP Chi-restraints excluded: chain B residue 503 GLU 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 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 404 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 603 ILE Chi-restraints excluded: chain C residue 635 HIS Chi-restraints excluded: chain D residue 204 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 309 VAL 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 503 GLU 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 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 529 VAL Chi-restraints excluded: chain F residue 536 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 204 VAL 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 480 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 243 VAL 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 439 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 522 GLN Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 595 ILE Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 132 HIS 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 345 GLU 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 439 SER Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 407 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 603 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 327 VAL Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 635 HIS Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain M residue 158 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 480 VAL Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 546 LEU 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 426 VAL Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 454 GLU Chi-restraints excluded: chain N residue 534 MET 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 291 THR Chi-restraints excluded: chain O residue 327 VAL Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 603 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 0.0170 chunk 621 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 537 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 584 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 599 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.191563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152966 restraints weight = 72143.882| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.90 r_work: 0.3699 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.6135 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= 0.244 Angle : 0.603 12.177 77175 Z= 0.304 Chirality : 0.046 0.222 9420 Planarity : 0.005 0.084 10065 Dihedral : 4.452 21.715 7875 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.05 % Favored : 92.74 % Rotamer: Outliers : 2.71 % Allowed : 20.90 % Favored : 76.39 % 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: -1.93 (0.10), residues: 7290 helix: 0.77 (0.11), residues: 2250 sheet: -2.41 (0.10), residues: 2655 loop : -1.64 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 341 HIS 0.006 0.001 HIS J 635 PHE 0.007 0.001 PHE D 450 TYR 0.021 0.002 TYR A 352 ARG 0.013 0.000 ARG B 181 =============================================================================== Job complete usr+sys time: 14283.02 seconds wall clock time: 247 minutes 13.75 seconds (14833.75 seconds total)