Starting phenix.real_space_refine on Thu Mar 21 08:46:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxi_29534/03_2024/8fxi_29534_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxi_29534/03_2024/8fxi_29534.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxi_29534/03_2024/8fxi_29534_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxi_29534/03_2024/8fxi_29534_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxi_29534/03_2024/8fxi_29534_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxi_29534/03_2024/8fxi_29534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxi_29534/03_2024/8fxi_29534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxi_29534/03_2024/8fxi_29534_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxi_29534/03_2024/8fxi_29534_neut_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 18884 2.51 5 N 4983 2.21 5 O 5680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "F ARG 15": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29641 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4777 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain breaks: 3 Chain: "B" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4921 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 25, 'TRANS': 589} Chain breaks: 1 Chain: "C" Number of atoms: 5033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5033 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 25, 'TRANS': 604} Chain: "D" Number of atoms: 5033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5033 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 25, 'TRANS': 604} Chain: "E" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4921 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 25, 'TRANS': 589} Chain breaks: 1 Chain: "F" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4777 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain breaks: 3 Chain: "G" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'YHZ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 14.03, per 1000 atoms: 0.47 Number of scatterers: 29641 At special positions: 0 Unit cell: (146.475, 180.225, 159.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 6 15.00 Mg 4 11.99 O 5680 8.00 N 4983 7.00 C 18884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.59 Conformation dependent library (CDL) restraints added in 5.2 seconds 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 38 sheets defined 29.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.58 Creating SS restraints... Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.667A pdb=" N ALA A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.982A pdb=" N LYS A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.625A pdb=" N ILE A 135 " --> pdb=" O TRP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.625A pdb=" N ALA A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.656A pdb=" N ASP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.744A pdb=" N LEU A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 366 through 372 Processing helix chain 'A' and resid 409 through 421 removed outlier: 4.704A pdb=" N HIS A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 478 removed outlier: 3.909A pdb=" N PHE A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 497 through 508 Processing helix chain 'A' and resid 537 through 545 removed outlier: 4.265A pdb=" N VAL A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 624 through 629 removed outlier: 3.999A pdb=" N LEU A 629 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 62 removed outlier: 3.555A pdb=" N VAL B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 Processing helix chain 'B' and resid 77 through 90 removed outlier: 4.032A pdb=" N LYS B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.940A pdb=" N ALA B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.945A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 363 through 370 removed outlier: 3.893A pdb=" N GLU B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 4.367A pdb=" N HIS B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 460 No H-bonds generated for 'chain 'B' and resid 457 through 460' Processing helix chain 'B' and resid 470 through 476 Processing helix chain 'B' and resid 482 through 485 Processing helix chain 'B' and resid 497 through 509 removed outlier: 3.515A pdb=" N MET B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 624 through 635 removed outlier: 4.073A pdb=" N LEU B 629 " --> pdb=" O GLN B 626 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS B 630 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 632 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 633 " --> pdb=" O LYS B 630 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 635 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.848A pdb=" N ASP C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 77 through 90 removed outlier: 4.118A pdb=" N LYS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 Processing helix chain 'C' and resid 144 through 155 Processing helix chain 'C' and resid 162 through 173 removed outlier: 3.817A pdb=" N ALA C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.774A pdb=" N ASP C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 removed outlier: 4.206A pdb=" N LEU C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 249 removed outlier: 3.534A pdb=" N GLU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 409 through 421 removed outlier: 4.425A pdb=" N HIS C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 477 removed outlier: 3.679A pdb=" N THR C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 485 Processing helix chain 'C' and resid 497 through 509 removed outlier: 3.615A pdb=" N LYS C 502 " --> pdb=" O ARG C 498 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 removed outlier: 4.323A pdb=" N VAL C 541 " --> pdb=" O TYR C 537 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 542 " --> pdb=" O ASN C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 564 Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 624 through 628 removed outlier: 3.901A pdb=" N TYR C 628 " --> pdb=" O GLU C 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 removed outlier: 3.848A pdb=" N ASP D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 77 through 90 removed outlier: 4.118A pdb=" N LYS D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 136 Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.818A pdb=" N ALA D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 208 through 215 removed outlier: 3.774A pdb=" N ASP D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 removed outlier: 4.205A pdb=" N LEU D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 249 removed outlier: 3.535A pdb=" N GLU D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 281 Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 409 through 421 removed outlier: 4.426A pdb=" N HIS D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 477 removed outlier: 3.679A pdb=" N THR D 477 " --> pdb=" O ARG D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 485 Processing helix chain 'D' and resid 497 through 509 removed outlier: 3.615A pdb=" N LYS D 502 " --> pdb=" O ARG D 498 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 546 removed outlier: 4.323A pdb=" N VAL D 541 " --> pdb=" O TYR D 537 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 542 " --> pdb=" O ASN D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 564 Processing helix chain 'D' and resid 584 through 588 Processing helix chain 'D' and resid 624 through 628 removed outlier: 3.902A pdb=" N TYR D 628 " --> pdb=" O GLU D 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 62 removed outlier: 3.555A pdb=" N VAL E 61 " --> pdb=" O ASN E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 70 Processing helix chain 'E' and resid 77 through 90 removed outlier: 4.031A pdb=" N LYS E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 136 Processing helix chain 'E' and resid 144 through 155 Processing helix chain 'E' and resid 162 through 173 removed outlier: 3.939A pdb=" N ALA E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.946A pdb=" N THR E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 226 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 335 through 344 Processing helix chain 'E' and resid 363 through 370 removed outlier: 3.893A pdb=" N GLU E 370 " --> pdb=" O HIS E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 421 removed outlier: 4.368A pdb=" N HIS E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 460 No H-bonds generated for 'chain 'E' and resid 457 through 460' Processing helix chain 'E' and resid 470 through 476 Processing helix chain 'E' and resid 482 through 485 Processing helix chain 'E' and resid 497 through 509 removed outlier: 3.516A pdb=" N MET E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 546 Processing helix chain 'E' and resid 559 through 564 Processing helix chain 'E' and resid 584 through 588 Processing helix chain 'E' and resid 624 through 635 removed outlier: 4.074A pdb=" N LEU E 629 " --> pdb=" O GLN E 626 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS E 630 " --> pdb=" O VAL E 627 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 632 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 633 " --> pdb=" O LYS E 630 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 635 " --> pdb=" O ILE E 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 65 removed outlier: 3.668A pdb=" N ALA F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL F 61 " --> pdb=" O ASN F 57 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 77 through 90 removed outlier: 3.983A pdb=" N LYS F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 135 removed outlier: 3.624A pdb=" N ILE F 135 " --> pdb=" O TRP F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 155 removed outlier: 3.626A pdb=" N ALA F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE F 149 " --> pdb=" O LYS F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'F' and resid 208 through 215 removed outlier: 3.656A pdb=" N ASP F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 227 removed outlier: 3.745A pdb=" N LEU F 227 " --> pdb=" O PHE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 Processing helix chain 'F' and resid 337 through 344 Processing helix chain 'F' and resid 366 through 372 Processing helix chain 'F' and resid 409 through 421 removed outlier: 4.703A pdb=" N HIS F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 478 removed outlier: 3.909A pdb=" N PHE F 478 " --> pdb=" O ILE F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 485 No H-bonds generated for 'chain 'F' and resid 483 through 485' Processing helix chain 'F' and resid 497 through 508 Processing helix chain 'F' and resid 537 through 545 removed outlier: 4.266A pdb=" N VAL F 541 " --> pdb=" O TYR F 537 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 542 " --> pdb=" O ASN F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 564 Processing helix chain 'F' and resid 586 through 588 No H-bonds generated for 'chain 'F' and resid 586 through 588' Processing helix chain 'F' and resid 624 through 629 removed outlier: 3.998A pdb=" N LEU F 629 " --> pdb=" O GLN F 626 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 20 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 Processing sheet with id= C, first strand: chain 'A' and resid 179 through 181 Processing sheet with id= D, first strand: chain 'A' and resid 399 through 402 removed outlier: 4.985A pdb=" N ASP A 306 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 449 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE A 432 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE A 447 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 488 through 492 removed outlier: 3.602A pdb=" N GLU A 556 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 574 through 578 removed outlier: 6.530A pdb=" N THR A 596 " --> pdb=" O VAL A 575 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU A 577 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 598 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 20 through 22 Processing sheet with id= H, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.691A pdb=" N ILE B 105 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.621A pdb=" N LEU B 186 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 399 through 402 removed outlier: 4.693A pdb=" N ASP B 306 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 433 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU B 449 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 432 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE B 447 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 488 through 492 removed outlier: 3.653A pdb=" N GLU B 556 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 574 through 578 removed outlier: 6.691A pdb=" N THR B 596 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N LEU B 577 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 598 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 20 through 23 Processing sheet with id= N, first strand: chain 'C' and resid 26 through 28 Processing sheet with id= O, first strand: chain 'C' and resid 179 through 181 removed outlier: 3.845A pdb=" N LEU C 186 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 234 through 237 removed outlier: 3.724A pdb=" N ASP C 235 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.957A pdb=" N LEU C 310 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA C 319 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG C 308 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU C 321 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP C 306 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 449 " --> pdb=" O ASP C 430 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE C 432 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE C 447 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 488 through 492 removed outlier: 3.539A pdb=" N GLU C 556 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 574 through 578 removed outlier: 6.585A pdb=" N THR C 596 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU C 577 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 598 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 20 through 23 Processing sheet with id= U, first strand: chain 'D' and resid 26 through 28 Processing sheet with id= V, first strand: chain 'D' and resid 179 through 181 removed outlier: 3.845A pdb=" N LEU D 186 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 234 through 237 removed outlier: 3.723A pdb=" N ASP D 235 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 398 through 402 removed outlier: 6.957A pdb=" N LEU D 310 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 319 " --> pdb=" O ARG D 308 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG D 308 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU D 321 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP D 306 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 449 " --> pdb=" O ASP D 430 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 432 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE D 447 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 488 through 492 removed outlier: 3.539A pdb=" N GLU D 556 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 574 through 578 removed outlier: 6.585A pdb=" N THR D 596 " --> pdb=" O VAL D 575 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU D 577 " --> pdb=" O THR D 596 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 598 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 20 through 22 Processing sheet with id= AB, first strand: chain 'E' and resid 25 through 28 removed outlier: 3.691A pdb=" N ILE E 105 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 179 through 181 removed outlier: 3.620A pdb=" N LEU E 186 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 399 through 402 removed outlier: 4.693A pdb=" N ASP E 306 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR E 433 " --> pdb=" O HIS E 305 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU E 449 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE E 432 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE E 447 " --> pdb=" O ILE E 432 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 488 through 492 removed outlier: 3.654A pdb=" N GLU E 556 " --> pdb=" O VAL E 519 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 574 through 578 removed outlier: 6.691A pdb=" N THR E 596 " --> pdb=" O VAL E 575 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N LEU E 577 " --> pdb=" O THR E 596 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE E 598 " --> pdb=" O LEU E 577 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 20 through 23 Processing sheet with id= AH, first strand: chain 'F' and resid 26 through 28 Processing sheet with id= AI, first strand: chain 'F' and resid 179 through 181 Processing sheet with id= AJ, first strand: chain 'F' and resid 399 through 402 removed outlier: 4.985A pdb=" N ASP F 306 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU F 449 " --> pdb=" O ASP F 430 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE F 432 " --> pdb=" O ILE F 447 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE F 447 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 488 through 492 removed outlier: 3.601A pdb=" N GLU F 556 " --> pdb=" O VAL F 519 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 574 through 578 removed outlier: 6.530A pdb=" N THR F 596 " --> pdb=" O VAL F 575 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU F 577 " --> pdb=" O THR F 596 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE F 598 " --> pdb=" O LEU F 577 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2454 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.64 Time building geometry restraints manager: 11.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.35: 9780 1.35 - 1.64: 20313 1.64 - 1.94: 136 1.94 - 2.23: 0 2.23 - 2.52: 1 Bond restraints: 30230 Sorted by residual: bond pdb=" C1' YHZ C 701 " pdb=" C8 YHZ C 701 " ideal model delta sigma weight residual 1.483 2.523 -1.040 2.00e-02 2.50e+03 2.71e+03 bond pdb=" C VAL B 327 " pdb=" N VAL B 328 " ideal model delta sigma weight residual 1.332 1.054 0.278 1.23e-02 6.61e+03 5.12e+02 bond pdb=" C VAL E 327 " pdb=" N VAL E 328 " ideal model delta sigma weight residual 1.332 1.054 0.278 1.23e-02 6.61e+03 5.12e+02 bond pdb=" C LYS D 257 " pdb=" N PRO D 258 " ideal model delta sigma weight residual 1.329 1.582 -0.253 1.20e-02 6.94e+03 4.45e+02 bond pdb=" C LYS C 257 " pdb=" N PRO C 258 " ideal model delta sigma weight residual 1.329 1.581 -0.253 1.20e-02 6.94e+03 4.44e+02 ... (remaining 30225 not shown) Histogram of bond angle deviations from ideal: 75.06 - 93.58: 55 93.58 - 112.11: 15081 112.11 - 130.63: 25676 130.63 - 149.15: 205 149.15 - 167.67: 8 Bond angle restraints: 41025 Sorted by residual: angle pdb=" N LEU C 376 " pdb=" CA LEU C 376 " pdb=" C LEU C 376 " ideal model delta sigma weight residual 112.68 158.89 -46.21 1.33e+00 5.65e-01 1.21e+03 angle pdb=" N LEU D 376 " pdb=" CA LEU D 376 " pdb=" C LEU D 376 " ideal model delta sigma weight residual 112.68 158.89 -46.21 1.33e+00 5.65e-01 1.21e+03 angle pdb=" N ALA E 279 " pdb=" CA ALA E 279 " pdb=" C ALA E 279 " ideal model delta sigma weight residual 111.28 145.49 -34.21 1.09e+00 8.42e-01 9.85e+02 angle pdb=" N ALA B 279 " pdb=" CA ALA B 279 " pdb=" C ALA B 279 " ideal model delta sigma weight residual 111.28 145.48 -34.20 1.09e+00 8.42e-01 9.85e+02 angle pdb=" O ASP A 377 " pdb=" C ASP A 377 " pdb=" N SER A 378 " ideal model delta sigma weight residual 122.48 87.55 34.93 1.21e+00 6.83e-01 8.33e+02 ... (remaining 41020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 17643 28.61 - 57.22: 489 57.22 - 85.82: 54 85.82 - 114.43: 14 114.43 - 143.04: 5 Dihedral angle restraints: 18205 sinusoidal: 7429 harmonic: 10776 Sorted by residual: dihedral pdb=" C GLU A 363 " pdb=" N GLU A 363 " pdb=" CA GLU A 363 " pdb=" CB GLU A 363 " ideal model delta harmonic sigma weight residual -122.60 -80.13 -42.47 0 2.50e+00 1.60e-01 2.89e+02 dihedral pdb=" C GLU F 363 " pdb=" N GLU F 363 " pdb=" CA GLU F 363 " pdb=" CB GLU F 363 " ideal model delta harmonic sigma weight residual -122.60 -80.13 -42.47 0 2.50e+00 1.60e-01 2.89e+02 dihedral pdb=" C ALA B 303 " pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" CB ALA B 303 " ideal model delta harmonic sigma weight residual -122.60 -85.52 -37.08 0 2.50e+00 1.60e-01 2.20e+02 ... (remaining 18202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.459: 4575 0.459 - 0.918: 42 0.918 - 1.377: 8 1.377 - 1.836: 4 1.836 - 2.294: 3 Chirality restraints: 4632 Sorted by residual: chirality pdb=" C1' YHZ C 701 " pdb=" C2' YHZ C 701 " pdb=" C8 YHZ C 701 " pdb=" O4' YHZ C 701 " both_signs ideal model delta sigma weight residual False 2.55 4.84 -2.29 2.00e-01 2.50e+01 1.32e+02 chirality pdb=" CA ILE A 297 " pdb=" N ILE A 297 " pdb=" C ILE A 297 " pdb=" CB ILE A 297 " both_signs ideal model delta sigma weight residual False 2.43 0.35 2.09 2.00e-01 2.50e+01 1.09e+02 chirality pdb=" CA ILE F 297 " pdb=" N ILE F 297 " pdb=" C ILE F 297 " pdb=" CB ILE F 297 " both_signs ideal model delta sigma weight residual False 2.43 0.35 2.09 2.00e-01 2.50e+01 1.09e+02 ... (remaining 4629 not shown) Planarity restraints: 5320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB 7ID H 2 " 0.160 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" CG 7ID H 2 " -0.096 2.00e-02 2.50e+03 pdb=" OD1 7ID H 2 " 0.114 2.00e-02 2.50e+03 pdb=" CA2 7ID H 2 " 0.348 2.00e-02 2.50e+03 pdb=" N2 7ID H 2 " -0.526 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB 7ID G 2 " -0.159 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" CG 7ID G 2 " 0.095 2.00e-02 2.50e+03 pdb=" OD1 7ID G 2 " -0.114 2.00e-02 2.50e+03 pdb=" CA2 7ID G 2 " -0.348 2.00e-02 2.50e+03 pdb=" N2 7ID G 2 " 0.526 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD2 7ID H 2 " -0.331 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" NE2 7ID H 2 " 0.505 2.00e-02 2.50e+03 pdb=" CZ2 7ID H 2 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 7ID H 2 " -0.173 2.00e-02 2.50e+03 pdb=" NH2 7ID H 2 " -0.086 2.00e-02 2.50e+03 ... (remaining 5317 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 57 2.42 - 3.04: 18127 3.04 - 3.66: 38100 3.66 - 4.28: 56250 4.28 - 4.90: 98799 Nonbonded interactions: 211333 Sorted by model distance: nonbonded pdb=" N THR A 385 " pdb=" O THR A 385 " model vdw 1.801 2.496 nonbonded pdb=" N THR F 385 " pdb=" O THR F 385 " model vdw 1.802 2.496 nonbonded pdb=" N GLU F 292 " pdb=" O GLU F 292 " model vdw 1.808 2.496 nonbonded pdb=" N GLU A 292 " pdb=" O GLU A 292 " model vdw 1.808 2.496 nonbonded pdb=" O GLU A 363 " pdb=" CB GLU A 363 " model vdw 1.931 2.752 ... (remaining 211328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 10 through 236 or resid 240 through 250 or resid 252 throu \ gh 254 or resid 278 through 285 or resid 292 through 636)) selection = (chain 'C' and (resid 10 through 236 or resid 240 through 250 or resid 252 throu \ gh 254 or resid 278 through 285 or resid 292 through 636)) selection = (chain 'D' and (resid 10 through 236 or resid 240 through 250 or resid 252 throu \ gh 254 or resid 278 through 285 or resid 292 through 636)) selection = (chain 'E' and (resid 10 through 236 or resid 240 through 250 or resid 252 throu \ gh 254 or resid 278 through 285 or resid 292 through 636)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 8.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 27.790 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 71.780 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.140 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:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 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 : 0.014 1.040 30230 Z= 0.935 Angle : 2.100 58.334 41025 Z= 1.422 Chirality : 0.124 2.294 4632 Planarity : 0.016 0.298 5320 Dihedral : 13.251 143.040 11253 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.07 % Favored : 92.08 % Rotamer: Outliers : 3.12 % Allowed : 7.30 % Favored : 89.58 % Cbeta Deviations : 2.68 % 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: -1.18 (0.14), residues: 3650 helix: 0.79 (0.17), residues: 1056 sheet: 0.47 (0.22), residues: 664 loop : -2.27 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 182 HIS 0.005 0.001 HIS E 208 PHE 0.014 0.002 PHE D 445 TYR 0.018 0.002 TYR E 252 ARG 0.004 0.000 ARG D 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 398 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.1720 (OUTLIER) cc_final: 0.1495 (mtp85) REVERT: A 113 ILE cc_start: 0.5568 (pt) cc_final: 0.5311 (mm) REVERT: A 217 LYS cc_start: 0.5172 (mttt) cc_final: 0.4840 (mmtt) REVERT: A 315 ARG cc_start: 0.5450 (mmm160) cc_final: 0.5168 (mmt180) REVERT: A 461 LYS cc_start: 0.5329 (tptt) cc_final: 0.4951 (pptt) REVERT: A 476 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6013 (tm-30) REVERT: A 483 LYS cc_start: 0.7061 (tttp) cc_final: 0.6858 (ptmm) REVERT: A 494 ARG cc_start: 0.5726 (ttp80) cc_final: 0.5342 (tpt90) REVERT: A 496 SER cc_start: 0.6115 (m) cc_final: 0.5860 (p) REVERT: A 546 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.4760 (tpt-90) REVERT: A 556 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.5922 (tm-30) REVERT: A 570 HIS cc_start: 0.6454 (t-90) cc_final: 0.5938 (t-170) REVERT: A 585 MET cc_start: 0.6943 (ttm) cc_final: 0.6741 (tpp) REVERT: B 152 GLN cc_start: 0.5997 (tp40) cc_final: 0.5618 (mm110) REVERT: B 173 GLU cc_start: 0.5825 (tt0) cc_final: 0.5600 (mt-10) REVERT: B 216 GLN cc_start: 0.6218 (mt0) cc_final: 0.5885 (mt0) REVERT: B 218 ASP cc_start: 0.7725 (m-30) cc_final: 0.7095 (t0) REVERT: B 227 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4785 (pp) REVERT: B 389 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.6021 (ptp-110) REVERT: B 405 ASN cc_start: 0.7737 (m-40) cc_final: 0.7330 (m-40) REVERT: B 473 ARG cc_start: 0.5686 (mmm160) cc_final: 0.5067 (mmp80) REVERT: B 480 GLU cc_start: 0.7018 (tt0) cc_final: 0.6501 (mp0) REVERT: B 483 LYS cc_start: 0.7755 (mttt) cc_final: 0.7168 (mmtp) REVERT: B 498 ARG cc_start: 0.5298 (ttt90) cc_final: 0.5095 (mpp-170) REVERT: B 501 GLN cc_start: 0.5808 (mt0) cc_final: 0.5571 (mt0) REVERT: B 502 LYS cc_start: 0.5641 (mmmm) cc_final: 0.5071 (mtpt) REVERT: B 505 ASP cc_start: 0.6003 (m-30) cc_final: 0.5536 (m-30) REVERT: B 535 ARG cc_start: 0.7129 (mmm160) cc_final: 0.6762 (tmm160) REVERT: B 582 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6701 (tp30) REVERT: B 594 ASP cc_start: 0.6387 (t70) cc_final: 0.6152 (p0) REVERT: B 603 ARG cc_start: 0.6381 (mtt180) cc_final: 0.6049 (tpt170) REVERT: B 604 GLU cc_start: 0.6502 (mt-10) cc_final: 0.5721 (mm-30) REVERT: B 614 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7171 (tt0) REVERT: B 615 GLN cc_start: 0.8223 (tt0) cc_final: 0.7990 (tt0) REVERT: B 619 GLU cc_start: 0.4878 (mt-10) cc_final: 0.4647 (pm20) REVERT: B 626 GLN cc_start: 0.7049 (mt0) cc_final: 0.6572 (mp10) REVERT: C 119 ARG cc_start: 0.5839 (ttm170) cc_final: 0.5149 (mtm-85) REVERT: C 123 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6245 (mm-30) REVERT: C 139 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7029 (mt-10) REVERT: C 216 GLN cc_start: 0.6553 (mt0) cc_final: 0.6100 (mt0) REVERT: C 222 LYS cc_start: 0.6363 (tttp) cc_final: 0.6127 (tttp) REVERT: C 466 GLU cc_start: 0.6874 (mt-10) cc_final: 0.5964 (pm20) REVERT: C 483 LYS cc_start: 0.7388 (mttt) cc_final: 0.6645 (tppt) REVERT: C 494 ARG cc_start: 0.7023 (ttm110) cc_final: 0.5654 (tpm170) REVERT: C 498 ARG cc_start: 0.6339 (mmm-85) cc_final: 0.5565 (ttp-110) REVERT: C 502 LYS cc_start: 0.6216 (ttmm) cc_final: 0.5558 (ttpp) REVERT: C 535 ARG cc_start: 0.6445 (mtp85) cc_final: 0.6048 (ptm160) REVERT: C 549 LYS cc_start: 0.7747 (mtpm) cc_final: 0.7068 (mttm) REVERT: C 567 MET cc_start: 0.8601 (mtm) cc_final: 0.8389 (mtp) REVERT: C 582 GLU cc_start: 0.7640 (tp30) cc_final: 0.6921 (tm-30) REVERT: C 604 GLU cc_start: 0.6365 (mm-30) cc_final: 0.5665 (mm-30) REVERT: C 610 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6590 (mttm) REVERT: C 614 GLU cc_start: 0.7105 (tt0) cc_final: 0.6708 (tt0) REVERT: C 617 GLU cc_start: 0.7034 (tt0) cc_final: 0.6686 (tt0) REVERT: C 626 GLN cc_start: 0.6248 (mm-40) cc_final: 0.6022 (mt0) REVERT: D 119 ARG cc_start: 0.5808 (ttm170) cc_final: 0.5123 (mtm-85) REVERT: D 123 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6292 (mm-30) REVERT: D 139 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7031 (mt-10) REVERT: D 216 GLN cc_start: 0.6547 (mt0) cc_final: 0.6089 (mt0) REVERT: D 222 LYS cc_start: 0.6359 (tttp) cc_final: 0.6123 (tttp) REVERT: D 466 GLU cc_start: 0.6877 (mt-10) cc_final: 0.5958 (pm20) REVERT: D 483 LYS cc_start: 0.7390 (mttt) cc_final: 0.6627 (tppt) REVERT: D 494 ARG cc_start: 0.7028 (ttm110) cc_final: 0.5672 (tpm170) REVERT: D 498 ARG cc_start: 0.6320 (mmm-85) cc_final: 0.5547 (ttp-110) REVERT: D 502 LYS cc_start: 0.6232 (ttmm) cc_final: 0.5573 (ttpp) REVERT: D 535 ARG cc_start: 0.6438 (mtp85) cc_final: 0.6045 (ptm160) REVERT: D 549 LYS cc_start: 0.7774 (mtpm) cc_final: 0.7084 (mttm) REVERT: D 567 MET cc_start: 0.8603 (mtm) cc_final: 0.8391 (mtp) REVERT: D 582 GLU cc_start: 0.7640 (tp30) cc_final: 0.6924 (tm-30) REVERT: D 604 GLU cc_start: 0.6369 (mm-30) cc_final: 0.5672 (mm-30) REVERT: D 610 LYS cc_start: 0.7053 (mtmt) cc_final: 0.6567 (mttm) REVERT: D 614 GLU cc_start: 0.7106 (tt0) cc_final: 0.6622 (tt0) REVERT: D 617 GLU cc_start: 0.7023 (tt0) cc_final: 0.6669 (tt0) REVERT: D 626 GLN cc_start: 0.6243 (mm-40) cc_final: 0.6010 (mt0) REVERT: E 152 GLN cc_start: 0.6022 (tp40) cc_final: 0.5559 (mm110) REVERT: E 173 GLU cc_start: 0.5839 (tt0) cc_final: 0.5621 (mt-10) REVERT: E 216 GLN cc_start: 0.6159 (mt0) cc_final: 0.5834 (mt0) REVERT: E 218 ASP cc_start: 0.7746 (m-30) cc_final: 0.7100 (t0) REVERT: E 227 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4802 (pp) REVERT: E 389 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.6038 (ptp-110) REVERT: E 405 ASN cc_start: 0.7734 (m-40) cc_final: 0.7327 (m-40) REVERT: E 473 ARG cc_start: 0.5713 (mmm160) cc_final: 0.5100 (mmp80) REVERT: E 480 GLU cc_start: 0.7028 (tt0) cc_final: 0.6496 (mp0) REVERT: E 483 LYS cc_start: 0.7753 (mttt) cc_final: 0.7182 (mmmm) REVERT: E 501 GLN cc_start: 0.5723 (mt0) cc_final: 0.5499 (mt0) REVERT: E 502 LYS cc_start: 0.5691 (mmmm) cc_final: 0.5120 (mtpt) REVERT: E 505 ASP cc_start: 0.6000 (m-30) cc_final: 0.5550 (m-30) REVERT: E 535 ARG cc_start: 0.7131 (mmm160) cc_final: 0.6759 (tmm160) REVERT: E 582 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6695 (tp30) REVERT: E 594 ASP cc_start: 0.6372 (t70) cc_final: 0.6148 (p0) REVERT: E 603 ARG cc_start: 0.6431 (mtt180) cc_final: 0.6019 (tpt170) REVERT: E 604 GLU cc_start: 0.6536 (mt-10) cc_final: 0.5751 (mm-30) REVERT: E 614 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7137 (tt0) REVERT: E 615 GLN cc_start: 0.8259 (tt0) cc_final: 0.7958 (tt0) REVERT: E 619 GLU cc_start: 0.4902 (mt-10) cc_final: 0.4657 (pm20) REVERT: E 626 GLN cc_start: 0.7074 (mt0) cc_final: 0.6551 (mp10) REVERT: F 11 ARG cc_start: 0.1811 (OUTLIER) cc_final: 0.1583 (mtp85) REVERT: F 113 ILE cc_start: 0.5617 (pt) cc_final: 0.5352 (mm) REVERT: F 217 LYS cc_start: 0.5230 (mttt) cc_final: 0.4853 (mmtt) REVERT: F 315 ARG cc_start: 0.5460 (mmm160) cc_final: 0.5182 (mmt180) REVERT: F 461 LYS cc_start: 0.5268 (tptt) cc_final: 0.4902 (pptt) REVERT: F 476 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6011 (tm-30) REVERT: F 483 LYS cc_start: 0.7033 (tttp) cc_final: 0.6818 (ptmm) REVERT: F 494 ARG cc_start: 0.5706 (ttp80) cc_final: 0.5319 (tpt90) REVERT: F 496 SER cc_start: 0.6120 (m) cc_final: 0.5873 (p) REVERT: F 546 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.4652 (mmm160) REVERT: F 556 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.5871 (tm-30) REVERT: F 570 HIS cc_start: 0.6452 (t-90) cc_final: 0.5952 (t-170) REVERT: F 585 MET cc_start: 0.6947 (ttm) cc_final: 0.6744 (tpp) outliers start: 100 outliers final: 28 residues processed: 492 average time/residue: 1.5583 time to fit residues: 882.3018 Evaluate side-chains 306 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 289 PRO Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 289 PRO Chi-restraints excluded: chain E residue 389 ARG Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 399 PHE Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 0.0770 chunk 277 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 187 optimal weight: 0.0980 chunk 148 optimal weight: 50.0000 chunk 286 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 332 optimal weight: 6.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 366 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN C 416 GLN C 501 GLN D 416 GLN D 501 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN F 300 ASN F 366 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30230 Z= 0.172 Angle : 0.618 11.064 41025 Z= 0.330 Chirality : 0.047 0.258 4632 Planarity : 0.005 0.054 5320 Dihedral : 11.317 179.644 4211 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.11 % Favored : 93.67 % Rotamer: Outliers : 2.56 % Allowed : 11.42 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3650 helix: 0.78 (0.17), residues: 1102 sheet: 0.56 (0.22), residues: 684 loop : -2.07 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 182 HIS 0.004 0.001 HIS F 366 PHE 0.012 0.001 PHE D 422 TYR 0.015 0.001 TYR D 332 ARG 0.003 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 274 time to evaluate : 3.935 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: A 37 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6566 (mt0) REVERT: A 217 LYS cc_start: 0.5061 (mttt) cc_final: 0.4778 (mmtm) REVERT: A 225 GLN cc_start: 0.6696 (tt0) cc_final: 0.6496 (tt0) REVERT: A 315 ARG cc_start: 0.5493 (mmm160) cc_final: 0.5173 (mmt180) REVERT: A 461 LYS cc_start: 0.5293 (tptt) cc_final: 0.4968 (pptt) REVERT: A 476 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6058 (tm-30) REVERT: A 483 LYS cc_start: 0.7187 (tttp) cc_final: 0.6938 (ptmm) REVERT: A 494 ARG cc_start: 0.5778 (ttp80) cc_final: 0.5447 (tpt90) REVERT: A 496 SER cc_start: 0.6393 (m) cc_final: 0.6038 (p) REVERT: A 546 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.4790 (mmm160) REVERT: A 559 GLU cc_start: 0.6148 (mt-10) cc_final: 0.5934 (mt-10) REVERT: A 570 HIS cc_start: 0.6325 (t-90) cc_final: 0.5904 (t-170) REVERT: B 152 GLN cc_start: 0.5797 (tp40) cc_final: 0.5507 (mm110) REVERT: B 173 GLU cc_start: 0.5790 (tt0) cc_final: 0.5588 (tt0) REVERT: B 194 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7385 (mm-40) REVERT: B 216 GLN cc_start: 0.6200 (mt0) cc_final: 0.5797 (mt0) REVERT: B 218 ASP cc_start: 0.7688 (m-30) cc_final: 0.7025 (OUTLIER) REVERT: B 227 LEU cc_start: 0.5095 (OUTLIER) cc_final: 0.4650 (pp) REVERT: B 405 ASN cc_start: 0.7730 (m-40) cc_final: 0.7334 (m-40) REVERT: B 473 ARG cc_start: 0.6160 (mmm160) cc_final: 0.5487 (mmp80) REVERT: B 480 GLU cc_start: 0.7056 (tt0) cc_final: 0.6545 (mp0) REVERT: B 483 LYS cc_start: 0.7811 (mttt) cc_final: 0.7183 (mmtp) REVERT: B 502 LYS cc_start: 0.5635 (mmmm) cc_final: 0.4961 (mtpt) REVERT: B 505 ASP cc_start: 0.6048 (m-30) cc_final: 0.5645 (t0) REVERT: B 535 ARG cc_start: 0.7116 (mmm160) cc_final: 0.6692 (tmm160) REVERT: B 582 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6630 (tp30) REVERT: B 594 ASP cc_start: 0.6355 (t70) cc_final: 0.6142 (p0) REVERT: B 603 ARG cc_start: 0.6334 (mtt180) cc_final: 0.5994 (tpt170) REVERT: B 604 GLU cc_start: 0.6558 (mt-10) cc_final: 0.5759 (mm-30) REVERT: B 614 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7129 (tt0) REVERT: B 619 GLU cc_start: 0.4825 (mt-10) cc_final: 0.4562 (mt-10) REVERT: B 626 GLN cc_start: 0.7020 (mt0) cc_final: 0.6487 (mp10) REVERT: C 119 ARG cc_start: 0.5737 (ttm170) cc_final: 0.5110 (mtm-85) REVERT: C 123 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6294 (mm-30) REVERT: C 139 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7050 (mt-10) REVERT: C 216 GLN cc_start: 0.6325 (mt0) cc_final: 0.5817 (mt0) REVERT: C 222 LYS cc_start: 0.6344 (tttp) cc_final: 0.6100 (tttp) REVERT: C 297 ILE cc_start: 0.5999 (OUTLIER) cc_final: 0.5782 (pp) REVERT: C 466 GLU cc_start: 0.6902 (mt-10) cc_final: 0.5990 (pm20) REVERT: C 483 LYS cc_start: 0.7315 (mttt) cc_final: 0.6659 (tppt) REVERT: C 494 ARG cc_start: 0.7033 (ttm110) cc_final: 0.5673 (tpm170) REVERT: C 498 ARG cc_start: 0.6252 (mmm-85) cc_final: 0.5481 (ttp-110) REVERT: C 502 LYS cc_start: 0.6046 (ttmm) cc_final: 0.5403 (ttpp) REVERT: C 535 ARG cc_start: 0.6392 (mtp85) cc_final: 0.5995 (ptm160) REVERT: C 549 LYS cc_start: 0.7816 (mtpm) cc_final: 0.7093 (mttm) REVERT: C 567 MET cc_start: 0.8651 (mtm) cc_final: 0.8294 (mtp) REVERT: C 581 SER cc_start: 0.7367 (m) cc_final: 0.7104 (p) REVERT: C 582 GLU cc_start: 0.7524 (tp30) cc_final: 0.7186 (tm-30) REVERT: C 590 ASP cc_start: 0.6671 (p0) cc_final: 0.5999 (m-30) REVERT: C 604 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5597 (mm-30) REVERT: C 610 LYS cc_start: 0.7161 (mtmt) cc_final: 0.6654 (mttm) REVERT: C 614 GLU cc_start: 0.7013 (tt0) cc_final: 0.6550 (tt0) REVERT: C 617 GLU cc_start: 0.6963 (tt0) cc_final: 0.6608 (tt0) REVERT: C 626 GLN cc_start: 0.6197 (mm-40) cc_final: 0.5962 (mt0) REVERT: D 119 ARG cc_start: 0.5747 (ttm170) cc_final: 0.5104 (mtm-85) REVERT: D 123 GLU cc_start: 0.6584 (mm-30) cc_final: 0.6308 (mm-30) REVERT: D 139 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7093 (mt-10) REVERT: D 216 GLN cc_start: 0.6367 (mt0) cc_final: 0.5860 (mt0) REVERT: D 222 LYS cc_start: 0.6333 (tttp) cc_final: 0.6091 (tttp) REVERT: D 297 ILE cc_start: 0.5947 (OUTLIER) cc_final: 0.5735 (pp) REVERT: D 466 GLU cc_start: 0.6878 (mt-10) cc_final: 0.5947 (pm20) REVERT: D 483 LYS cc_start: 0.7318 (mttt) cc_final: 0.6664 (tppt) REVERT: D 494 ARG cc_start: 0.7031 (ttm110) cc_final: 0.5672 (tpm170) REVERT: D 498 ARG cc_start: 0.6252 (mmm-85) cc_final: 0.5483 (ttp-110) REVERT: D 502 LYS cc_start: 0.6074 (ttmm) cc_final: 0.5434 (ttpp) REVERT: D 535 ARG cc_start: 0.6399 (mtp85) cc_final: 0.5998 (ptm160) REVERT: D 549 LYS cc_start: 0.7805 (mtpm) cc_final: 0.7084 (mttm) REVERT: D 567 MET cc_start: 0.8652 (mtm) cc_final: 0.8295 (mtp) REVERT: D 581 SER cc_start: 0.7356 (m) cc_final: 0.7094 (p) REVERT: D 582 GLU cc_start: 0.7526 (tp30) cc_final: 0.7185 (tm-30) REVERT: D 590 ASP cc_start: 0.6668 (p0) cc_final: 0.5995 (m-30) REVERT: D 604 GLU cc_start: 0.6256 (mm-30) cc_final: 0.5593 (mm-30) REVERT: D 610 LYS cc_start: 0.7159 (mtmt) cc_final: 0.6653 (mttm) REVERT: D 614 GLU cc_start: 0.7006 (tt0) cc_final: 0.6541 (tt0) REVERT: D 617 GLU cc_start: 0.6964 (tt0) cc_final: 0.6609 (tt0) REVERT: D 626 GLN cc_start: 0.6263 (mm-40) cc_final: 0.6036 (mt0) REVERT: E 152 GLN cc_start: 0.5877 (tp40) cc_final: 0.5551 (mm110) REVERT: E 194 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7394 (mm-40) REVERT: E 216 GLN cc_start: 0.6189 (mt0) cc_final: 0.5784 (mt0) REVERT: E 218 ASP cc_start: 0.7672 (m-30) cc_final: 0.7011 (OUTLIER) REVERT: E 227 LEU cc_start: 0.5105 (OUTLIER) cc_final: 0.4662 (pp) REVERT: E 405 ASN cc_start: 0.7727 (m-40) cc_final: 0.7373 (m-40) REVERT: E 473 ARG cc_start: 0.6221 (mmm160) cc_final: 0.5546 (mmp80) REVERT: E 480 GLU cc_start: 0.7100 (tt0) cc_final: 0.6592 (mp0) REVERT: E 483 LYS cc_start: 0.7815 (mttt) cc_final: 0.7184 (mmtp) REVERT: E 502 LYS cc_start: 0.5693 (mmmm) cc_final: 0.5019 (mtpt) REVERT: E 505 ASP cc_start: 0.5988 (m-30) cc_final: 0.5574 (t0) REVERT: E 535 ARG cc_start: 0.7136 (mmm160) cc_final: 0.6717 (tmm160) REVERT: E 582 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6661 (tp30) REVERT: E 603 ARG cc_start: 0.6317 (mtt180) cc_final: 0.5944 (mmp-170) REVERT: E 604 GLU cc_start: 0.6670 (mt-10) cc_final: 0.5878 (mm-30) REVERT: E 614 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7108 (tt0) REVERT: E 626 GLN cc_start: 0.7019 (mt0) cc_final: 0.6497 (mp10) REVERT: F 108 ILE cc_start: 0.5340 (mt) cc_final: 0.5121 (pt) REVERT: F 217 LYS cc_start: 0.5129 (mttt) cc_final: 0.4799 (mmtm) REVERT: F 315 ARG cc_start: 0.5489 (mmm160) cc_final: 0.5182 (mmt180) REVERT: F 461 LYS cc_start: 0.5342 (tptt) cc_final: 0.4974 (pptt) REVERT: F 476 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6057 (tm-30) REVERT: F 483 LYS cc_start: 0.7195 (tttp) cc_final: 0.6927 (ptmm) REVERT: F 494 ARG cc_start: 0.5779 (ttp80) cc_final: 0.5358 (tpt90) REVERT: F 496 SER cc_start: 0.6402 (m) cc_final: 0.6035 (p) REVERT: F 546 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.4773 (mmm160) REVERT: F 570 HIS cc_start: 0.6210 (t-90) cc_final: 0.5860 (t-170) REVERT: F 590 ASP cc_start: 0.5681 (OUTLIER) cc_final: 0.5320 (m-30) outliers start: 82 outliers final: 33 residues processed: 337 average time/residue: 1.5680 time to fit residues: 608.2599 Evaluate side-chains 289 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 248 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 91 optimal weight: 0.0030 chunk 332 optimal weight: 20.0000 chunk 359 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 330 optimal weight: 40.0000 chunk 113 optimal weight: 5.9990 chunk 267 optimal weight: 0.0980 overall best weight: 2.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN B 37 GLN B 156 ASN B 451 ASN E 89 ASN E 156 ASN E 451 ASN F 225 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30230 Z= 0.352 Angle : 0.720 10.212 41025 Z= 0.385 Chirality : 0.052 0.257 4632 Planarity : 0.006 0.059 5320 Dihedral : 11.046 177.466 4176 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.60 % Rotamer: Outliers : 3.62 % Allowed : 12.14 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.21 (0.14), residues: 3650 helix: 0.45 (0.16), residues: 1108 sheet: 0.39 (0.21), residues: 708 loop : -2.18 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 129 HIS 0.006 0.002 HIS E 421 PHE 0.028 0.003 PHE C 445 TYR 0.030 0.002 TYR D 165 ARG 0.006 0.001 ARG D 494 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 241 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.6847 (ttm170) cc_final: 0.6407 (ttm-80) REVERT: A 217 LYS cc_start: 0.5117 (mttt) cc_final: 0.4808 (mmtt) REVERT: A 315 ARG cc_start: 0.5640 (mmm160) cc_final: 0.5244 (mmt-90) REVERT: A 413 ILE cc_start: 0.4659 (OUTLIER) cc_final: 0.4414 (mp) REVERT: A 461 LYS cc_start: 0.5323 (tptt) cc_final: 0.4904 (pptt) REVERT: A 476 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6066 (tm-30) REVERT: A 483 LYS cc_start: 0.7194 (tttp) cc_final: 0.6942 (ptmm) REVERT: A 494 ARG cc_start: 0.5848 (ttp80) cc_final: 0.5405 (tpt90) REVERT: A 546 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5108 (mmm160) REVERT: A 556 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6357 (tm-30) REVERT: A 570 HIS cc_start: 0.6412 (t-90) cc_final: 0.6044 (t-170) REVERT: B 152 GLN cc_start: 0.5962 (tp40) cc_final: 0.5670 (mm110) REVERT: B 173 GLU cc_start: 0.6027 (tt0) cc_final: 0.5800 (tt0) REVERT: B 216 GLN cc_start: 0.6320 (mt0) cc_final: 0.5902 (mt0) REVERT: B 218 ASP cc_start: 0.7723 (m-30) cc_final: 0.7170 (OUTLIER) REVERT: B 222 LYS cc_start: 0.5703 (mttm) cc_final: 0.5100 (mtpp) REVERT: B 227 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4262 (pp) REVERT: B 405 ASN cc_start: 0.7753 (m-40) cc_final: 0.7363 (m-40) REVERT: B 473 ARG cc_start: 0.6356 (mmm160) cc_final: 0.5573 (mmp80) REVERT: B 480 GLU cc_start: 0.7055 (tt0) cc_final: 0.6520 (mp0) REVERT: B 483 LYS cc_start: 0.7898 (mttt) cc_final: 0.7235 (mmtp) REVERT: B 502 LYS cc_start: 0.5703 (mmmm) cc_final: 0.5124 (mtpt) REVERT: B 505 ASP cc_start: 0.6014 (m-30) cc_final: 0.5607 (m-30) REVERT: B 535 ARG cc_start: 0.7141 (mmm160) cc_final: 0.6766 (tmm160) REVERT: B 582 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6563 (tp30) REVERT: B 594 ASP cc_start: 0.6424 (t70) cc_final: 0.6051 (p0) REVERT: B 603 ARG cc_start: 0.6565 (mtt180) cc_final: 0.5989 (mtp85) REVERT: B 604 GLU cc_start: 0.6676 (mt-10) cc_final: 0.5832 (mm-30) REVERT: B 614 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7209 (tt0) REVERT: B 626 GLN cc_start: 0.7110 (mt0) cc_final: 0.6512 (mp10) REVERT: C 119 ARG cc_start: 0.6163 (ttm170) cc_final: 0.5300 (mtm-85) REVERT: C 123 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6325 (mm-30) REVERT: C 139 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6853 (mt-10) REVERT: C 222 LYS cc_start: 0.6410 (tttp) cc_final: 0.6160 (tttp) REVERT: C 297 ILE cc_start: 0.5718 (OUTLIER) cc_final: 0.5493 (pp) REVERT: C 466 GLU cc_start: 0.6811 (mt-10) cc_final: 0.5819 (pm20) REVERT: C 483 LYS cc_start: 0.7163 (mttt) cc_final: 0.6553 (tppt) REVERT: C 494 ARG cc_start: 0.7013 (ttm110) cc_final: 0.5684 (tpm170) REVERT: C 498 ARG cc_start: 0.6346 (mmm-85) cc_final: 0.5623 (ttp80) REVERT: C 502 LYS cc_start: 0.6158 (ttmm) cc_final: 0.5465 (ttpp) REVERT: C 535 ARG cc_start: 0.6478 (mtp85) cc_final: 0.6059 (ptm160) REVERT: C 549 LYS cc_start: 0.7975 (mtpm) cc_final: 0.7250 (mttm) REVERT: C 582 GLU cc_start: 0.7293 (tp30) cc_final: 0.7012 (tm-30) REVERT: C 590 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6420 (m-30) REVERT: C 604 GLU cc_start: 0.6208 (mm-30) cc_final: 0.5549 (mm-30) REVERT: C 614 GLU cc_start: 0.7146 (tt0) cc_final: 0.6713 (tt0) REVERT: C 617 GLU cc_start: 0.7069 (tt0) cc_final: 0.6708 (tt0) REVERT: C 626 GLN cc_start: 0.6218 (mm-40) cc_final: 0.5993 (mt0) REVERT: D 119 ARG cc_start: 0.6162 (ttm170) cc_final: 0.5300 (mtm-85) REVERT: D 123 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6320 (mm-30) REVERT: D 139 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6895 (mt-10) REVERT: D 297 ILE cc_start: 0.5718 (OUTLIER) cc_final: 0.5497 (pp) REVERT: D 466 GLU cc_start: 0.6810 (mt-10) cc_final: 0.5824 (pm20) REVERT: D 483 LYS cc_start: 0.7164 (mttt) cc_final: 0.6554 (tppt) REVERT: D 494 ARG cc_start: 0.7012 (ttm110) cc_final: 0.5682 (tpm170) REVERT: D 498 ARG cc_start: 0.6359 (mmm-85) cc_final: 0.5630 (ttp80) REVERT: D 502 LYS cc_start: 0.6160 (ttmm) cc_final: 0.5468 (ttpp) REVERT: D 535 ARG cc_start: 0.6477 (mtp85) cc_final: 0.6061 (ptm160) REVERT: D 549 LYS cc_start: 0.7973 (mtpm) cc_final: 0.7247 (mttm) REVERT: D 582 GLU cc_start: 0.7292 (tp30) cc_final: 0.7010 (tm-30) REVERT: D 590 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6418 (m-30) REVERT: D 604 GLU cc_start: 0.6210 (mm-30) cc_final: 0.5551 (mm-30) REVERT: D 614 GLU cc_start: 0.7147 (tt0) cc_final: 0.6712 (tt0) REVERT: D 617 GLU cc_start: 0.7070 (tt0) cc_final: 0.6710 (tt0) REVERT: D 626 GLN cc_start: 0.6229 (mm-40) cc_final: 0.5983 (mt0) REVERT: E 152 GLN cc_start: 0.5892 (tp40) cc_final: 0.5602 (mm110) REVERT: E 216 GLN cc_start: 0.6276 (mt0) cc_final: 0.5870 (mt0) REVERT: E 218 ASP cc_start: 0.7722 (m-30) cc_final: 0.7154 (OUTLIER) REVERT: E 222 LYS cc_start: 0.5702 (mttm) cc_final: 0.5097 (mtpp) REVERT: E 227 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4262 (pp) REVERT: E 405 ASN cc_start: 0.7764 (m-40) cc_final: 0.7364 (m-40) REVERT: E 473 ARG cc_start: 0.6354 (mmm160) cc_final: 0.5636 (mmp80) REVERT: E 480 GLU cc_start: 0.7060 (tt0) cc_final: 0.6524 (mp0) REVERT: E 483 LYS cc_start: 0.7897 (mttt) cc_final: 0.7234 (mmtp) REVERT: E 502 LYS cc_start: 0.5688 (mmmm) cc_final: 0.5063 (mtpt) REVERT: E 535 ARG cc_start: 0.7165 (mmm160) cc_final: 0.6787 (tmm160) REVERT: E 582 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6563 (tp30) REVERT: E 603 ARG cc_start: 0.6580 (mtt180) cc_final: 0.6009 (mtp85) REVERT: E 604 GLU cc_start: 0.6669 (mt-10) cc_final: 0.5831 (mm-30) REVERT: E 614 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7211 (tt0) REVERT: E 626 GLN cc_start: 0.7101 (mt0) cc_final: 0.6554 (mp10) REVERT: F 217 LYS cc_start: 0.5124 (mttt) cc_final: 0.4813 (mmtt) REVERT: F 315 ARG cc_start: 0.5612 (mmm160) cc_final: 0.5249 (mmt-90) REVERT: F 413 ILE cc_start: 0.4683 (OUTLIER) cc_final: 0.4438 (mp) REVERT: F 461 LYS cc_start: 0.5316 (tptt) cc_final: 0.4938 (pptt) REVERT: F 476 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6081 (tm-30) REVERT: F 483 LYS cc_start: 0.7168 (tttp) cc_final: 0.6929 (ptmm) REVERT: F 494 ARG cc_start: 0.5850 (ttp80) cc_final: 0.5405 (tpt90) REVERT: F 546 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5106 (mmm160) REVERT: F 556 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6347 (tm-30) REVERT: F 570 HIS cc_start: 0.6351 (t-90) cc_final: 0.6033 (t-170) REVERT: F 590 ASP cc_start: 0.5691 (OUTLIER) cc_final: 0.5348 (m-30) outliers start: 116 outliers final: 41 residues processed: 339 average time/residue: 1.7156 time to fit residues: 664.7545 Evaluate side-chains 274 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 222 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 609 ARG Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 609 ARG Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 590 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 158 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 334 optimal weight: 0.9980 chunk 353 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30230 Z= 0.149 Angle : 0.537 8.441 41025 Z= 0.290 Chirality : 0.046 0.274 4632 Planarity : 0.004 0.051 5320 Dihedral : 10.118 171.654 4162 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.25 % Favored : 93.59 % Rotamer: Outliers : 2.84 % Allowed : 14.26 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3650 helix: 0.67 (0.16), residues: 1116 sheet: 0.58 (0.22), residues: 700 loop : -2.06 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 182 HIS 0.003 0.001 HIS F 305 PHE 0.012 0.001 PHE D 445 TYR 0.015 0.001 TYR D 165 ARG 0.003 0.000 ARG F 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 231 time to evaluate : 3.485 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: A 55 ILE cc_start: 0.3160 (OUTLIER) cc_final: 0.2924 (tt) REVERT: A 217 LYS cc_start: 0.4828 (mttt) cc_final: 0.4570 (mmtt) REVERT: A 315 ARG cc_start: 0.5525 (mmm160) cc_final: 0.5156 (mmt-90) REVERT: A 461 LYS cc_start: 0.5305 (tptt) cc_final: 0.4912 (pptt) REVERT: A 476 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5998 (tm-30) REVERT: A 483 LYS cc_start: 0.7042 (tttp) cc_final: 0.6791 (ptmm) REVERT: A 494 ARG cc_start: 0.5938 (ttp80) cc_final: 0.5470 (tpt90) REVERT: A 496 SER cc_start: 0.6807 (OUTLIER) cc_final: 0.5734 (p) REVERT: A 522 GLU cc_start: 0.6230 (pm20) cc_final: 0.5930 (pm20) REVERT: A 546 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5225 (mmm160) REVERT: A 556 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: A 570 HIS cc_start: 0.6365 (t-90) cc_final: 0.6011 (t-170) REVERT: B 152 GLN cc_start: 0.5855 (tp40) cc_final: 0.5527 (mm110) REVERT: B 216 GLN cc_start: 0.6125 (mt0) cc_final: 0.5673 (mt0) REVERT: B 218 ASP cc_start: 0.7720 (m-30) cc_final: 0.6983 (OUTLIER) REVERT: B 227 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4530 (pp) REVERT: B 405 ASN cc_start: 0.7718 (m-40) cc_final: 0.7293 (m-40) REVERT: B 473 ARG cc_start: 0.6266 (mmm160) cc_final: 0.5516 (mpp-170) REVERT: B 480 GLU cc_start: 0.7114 (tt0) cc_final: 0.6623 (mp0) REVERT: B 483 LYS cc_start: 0.7896 (mttt) cc_final: 0.7217 (mmtp) REVERT: B 502 LYS cc_start: 0.5659 (mmmm) cc_final: 0.5043 (mtpt) REVERT: B 535 ARG cc_start: 0.7146 (mmm160) cc_final: 0.6787 (tmm160) REVERT: B 582 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6511 (tp30) REVERT: B 594 ASP cc_start: 0.6224 (t70) cc_final: 0.5976 (p0) REVERT: B 603 ARG cc_start: 0.6514 (mtt180) cc_final: 0.5884 (mtp85) REVERT: B 604 GLU cc_start: 0.6724 (mt-10) cc_final: 0.5867 (mm-30) REVERT: B 614 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7155 (tt0) REVERT: B 626 GLN cc_start: 0.7082 (mt0) cc_final: 0.6450 (mp10) REVERT: C 119 ARG cc_start: 0.5875 (ttm170) cc_final: 0.5130 (mtm-85) REVERT: C 123 GLU cc_start: 0.6505 (mm-30) cc_final: 0.6196 (mm-30) REVERT: C 139 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6932 (mt-10) REVERT: C 184 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: C 222 LYS cc_start: 0.6227 (tttp) cc_final: 0.5965 (tttp) REVERT: C 297 ILE cc_start: 0.5527 (OUTLIER) cc_final: 0.5326 (pp) REVERT: C 466 GLU cc_start: 0.6840 (mt-10) cc_final: 0.5792 (pm20) REVERT: C 483 LYS cc_start: 0.7205 (mttt) cc_final: 0.6594 (tppt) REVERT: C 494 ARG cc_start: 0.6995 (ttm110) cc_final: 0.5686 (tpm170) REVERT: C 498 ARG cc_start: 0.5979 (mmm-85) cc_final: 0.5189 (ttp80) REVERT: C 502 LYS cc_start: 0.5995 (ttmm) cc_final: 0.5334 (ttpp) REVERT: C 535 ARG cc_start: 0.6405 (mtp85) cc_final: 0.6022 (ptm160) REVERT: C 549 LYS cc_start: 0.7871 (mtpm) cc_final: 0.7076 (mttm) REVERT: C 581 SER cc_start: 0.6818 (m) cc_final: 0.6448 (p) REVERT: C 582 GLU cc_start: 0.7237 (tp30) cc_final: 0.6954 (tm-30) REVERT: C 590 ASP cc_start: 0.6562 (p0) cc_final: 0.6118 (m-30) REVERT: C 604 GLU cc_start: 0.6149 (mm-30) cc_final: 0.5490 (mm-30) REVERT: C 614 GLU cc_start: 0.7056 (tt0) cc_final: 0.5321 (mp0) REVERT: C 617 GLU cc_start: 0.6917 (tt0) cc_final: 0.6565 (tt0) REVERT: C 626 GLN cc_start: 0.6212 (mm-40) cc_final: 0.5980 (mt0) REVERT: D 119 ARG cc_start: 0.5870 (ttm170) cc_final: 0.5131 (mtm-85) REVERT: D 123 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6199 (mm-30) REVERT: D 139 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6965 (mt-10) REVERT: D 184 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: D 222 LYS cc_start: 0.6217 (tttp) cc_final: 0.5955 (tttp) REVERT: D 297 ILE cc_start: 0.5528 (OUTLIER) cc_final: 0.5326 (pp) REVERT: D 466 GLU cc_start: 0.6791 (mt-10) cc_final: 0.5754 (pm20) REVERT: D 483 LYS cc_start: 0.7204 (mttt) cc_final: 0.6595 (tppt) REVERT: D 494 ARG cc_start: 0.6995 (ttm110) cc_final: 0.5686 (tpm170) REVERT: D 498 ARG cc_start: 0.5959 (mmm-85) cc_final: 0.5195 (ttp80) REVERT: D 502 LYS cc_start: 0.5992 (ttmm) cc_final: 0.5332 (ttpp) REVERT: D 535 ARG cc_start: 0.6394 (mtp85) cc_final: 0.6015 (ptm160) REVERT: D 549 LYS cc_start: 0.7868 (mtpm) cc_final: 0.7074 (mttm) REVERT: D 581 SER cc_start: 0.6821 (m) cc_final: 0.6451 (p) REVERT: D 582 GLU cc_start: 0.7231 (tp30) cc_final: 0.6946 (tm-30) REVERT: D 590 ASP cc_start: 0.6559 (p0) cc_final: 0.6115 (m-30) REVERT: D 604 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5497 (mm-30) REVERT: D 614 GLU cc_start: 0.7052 (tt0) cc_final: 0.5314 (mp0) REVERT: D 617 GLU cc_start: 0.6941 (tt0) cc_final: 0.6590 (tt0) REVERT: D 626 GLN cc_start: 0.6208 (mm-40) cc_final: 0.5976 (mt0) REVERT: E 152 GLN cc_start: 0.5829 (tp40) cc_final: 0.5510 (mm110) REVERT: E 216 GLN cc_start: 0.6126 (mt0) cc_final: 0.5677 (mt0) REVERT: E 218 ASP cc_start: 0.7718 (m-30) cc_final: 0.6969 (OUTLIER) REVERT: E 227 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4500 (pp) REVERT: E 405 ASN cc_start: 0.7717 (m-40) cc_final: 0.7294 (m-40) REVERT: E 473 ARG cc_start: 0.6263 (mmm160) cc_final: 0.5513 (mpp-170) REVERT: E 480 GLU cc_start: 0.7079 (tt0) cc_final: 0.6606 (mp0) REVERT: E 483 LYS cc_start: 0.7883 (mttt) cc_final: 0.7199 (mmtp) REVERT: E 502 LYS cc_start: 0.5661 (mmmm) cc_final: 0.5045 (mtpt) REVERT: E 535 ARG cc_start: 0.7157 (mmm160) cc_final: 0.6824 (ttp80) REVERT: E 582 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6478 (tp30) REVERT: E 603 ARG cc_start: 0.6511 (mtt180) cc_final: 0.5888 (mtp85) REVERT: E 604 GLU cc_start: 0.6709 (mt-10) cc_final: 0.5863 (mm-30) REVERT: E 614 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7157 (tt0) REVERT: E 626 GLN cc_start: 0.7038 (mt0) cc_final: 0.6432 (mp10) REVERT: F 55 ILE cc_start: 0.3175 (OUTLIER) cc_final: 0.2946 (tt) REVERT: F 217 LYS cc_start: 0.4837 (mttt) cc_final: 0.4579 (mmtt) REVERT: F 461 LYS cc_start: 0.5326 (tptt) cc_final: 0.4944 (pptt) REVERT: F 476 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6004 (tm-30) REVERT: F 483 LYS cc_start: 0.7128 (tttp) cc_final: 0.6863 (ptmm) REVERT: F 494 ARG cc_start: 0.5940 (ttp80) cc_final: 0.5462 (tpt90) REVERT: F 496 SER cc_start: 0.6799 (OUTLIER) cc_final: 0.5746 (p) REVERT: F 522 GLU cc_start: 0.6214 (pm20) cc_final: 0.5972 (pm20) REVERT: F 546 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5189 (mmm160) REVERT: F 556 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6329 (tm-30) REVERT: F 570 HIS cc_start: 0.6254 (t-90) cc_final: 0.5953 (t-170) REVERT: F 590 ASP cc_start: 0.5677 (OUTLIER) cc_final: 0.5312 (m-30) outliers start: 91 outliers final: 42 residues processed: 308 average time/residue: 1.6394 time to fit residues: 577.3991 Evaluate side-chains 277 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 222 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 590 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 0.5980 chunk 200 optimal weight: 0.0270 chunk 5 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 145 optimal weight: 0.0010 chunk 301 optimal weight: 0.0870 chunk 244 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 180 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 overall best weight: 0.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN F 24 ASN F 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30230 Z= 0.124 Angle : 0.487 7.661 41025 Z= 0.262 Chirality : 0.045 0.255 4632 Planarity : 0.004 0.046 5320 Dihedral : 9.654 172.338 4162 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.30 % Favored : 93.53 % Rotamer: Outliers : 2.68 % Allowed : 14.92 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3650 helix: 0.84 (0.17), residues: 1128 sheet: 0.70 (0.22), residues: 700 loop : -1.91 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 182 HIS 0.002 0.001 HIS E 208 PHE 0.009 0.001 PHE D 445 TYR 0.013 0.001 TYR B 628 ARG 0.003 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 230 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.2518 (OUTLIER) cc_final: 0.2139 (mtp85) REVERT: A 37 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6589 (mt0) REVERT: A 55 ILE cc_start: 0.3104 (OUTLIER) cc_final: 0.2765 (tt) REVERT: A 217 LYS cc_start: 0.4830 (mttt) cc_final: 0.4558 (mmtt) REVERT: A 461 LYS cc_start: 0.5305 (tptt) cc_final: 0.4944 (pptt) REVERT: A 476 GLU cc_start: 0.6435 (mt-10) cc_final: 0.5992 (tm-30) REVERT: A 483 LYS cc_start: 0.7088 (tttp) cc_final: 0.6849 (ptmm) REVERT: A 494 ARG cc_start: 0.5933 (ttp80) cc_final: 0.5469 (tpt90) REVERT: A 496 SER cc_start: 0.6895 (OUTLIER) cc_final: 0.5822 (p) REVERT: A 522 GLU cc_start: 0.6070 (pm20) cc_final: 0.5787 (pm20) REVERT: A 546 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5278 (mmm160) REVERT: A 556 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6271 (tm-30) REVERT: A 570 HIS cc_start: 0.6256 (t-90) cc_final: 0.5976 (t-170) REVERT: B 152 GLN cc_start: 0.5807 (tp40) cc_final: 0.5481 (mm110) REVERT: B 194 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7285 (mm-40) REVERT: B 216 GLN cc_start: 0.6143 (mt0) cc_final: 0.5673 (mt0) REVERT: B 218 ASP cc_start: 0.7681 (m-30) cc_final: 0.6963 (OUTLIER) REVERT: B 227 LEU cc_start: 0.4915 (OUTLIER) cc_final: 0.4430 (pp) REVERT: B 405 ASN cc_start: 0.7703 (m-40) cc_final: 0.7262 (m-40) REVERT: B 473 ARG cc_start: 0.6253 (mmm160) cc_final: 0.5497 (mpp-170) REVERT: B 480 GLU cc_start: 0.7106 (tt0) cc_final: 0.6586 (mp0) REVERT: B 483 LYS cc_start: 0.7882 (mttt) cc_final: 0.7195 (mmmm) REVERT: B 502 LYS cc_start: 0.5673 (mmmm) cc_final: 0.5102 (mtpt) REVERT: B 505 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.5622 (m-30) REVERT: B 535 ARG cc_start: 0.7152 (mmm160) cc_final: 0.6828 (ttp80) REVERT: B 582 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6435 (tp30) REVERT: B 594 ASP cc_start: 0.6264 (t70) cc_final: 0.5979 (p0) REVERT: B 603 ARG cc_start: 0.6461 (mtt180) cc_final: 0.5802 (mmp-170) REVERT: B 604 GLU cc_start: 0.6676 (mt-10) cc_final: 0.5821 (mm-30) REVERT: B 614 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7131 (tt0) REVERT: B 626 GLN cc_start: 0.7025 (mt0) cc_final: 0.6396 (mp10) REVERT: C 119 ARG cc_start: 0.5745 (ttm170) cc_final: 0.5049 (mtm-85) REVERT: C 123 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6253 (mm-30) REVERT: C 139 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6959 (mt-10) REVERT: C 257 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7499 (mmtt) REVERT: C 466 GLU cc_start: 0.6850 (mt-10) cc_final: 0.5799 (pm20) REVERT: C 483 LYS cc_start: 0.7247 (mttt) cc_final: 0.6626 (tppt) REVERT: C 494 ARG cc_start: 0.7030 (ttm110) cc_final: 0.5722 (tpm170) REVERT: C 498 ARG cc_start: 0.5890 (mmm-85) cc_final: 0.5122 (ttp80) REVERT: C 502 LYS cc_start: 0.5983 (ttmm) cc_final: 0.5319 (ttpp) REVERT: C 535 ARG cc_start: 0.6375 (mtp85) cc_final: 0.6012 (ptm160) REVERT: C 549 LYS cc_start: 0.7840 (mtpm) cc_final: 0.7024 (mttm) REVERT: C 581 SER cc_start: 0.6593 (m) cc_final: 0.6263 (p) REVERT: C 582 GLU cc_start: 0.7191 (tp30) cc_final: 0.6893 (tm-30) REVERT: C 590 ASP cc_start: 0.6495 (p0) cc_final: 0.6150 (m-30) REVERT: C 604 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5508 (mm-30) REVERT: C 614 GLU cc_start: 0.7022 (tt0) cc_final: 0.5316 (mp0) REVERT: C 617 GLU cc_start: 0.6910 (tt0) cc_final: 0.6600 (tt0) REVERT: C 626 GLN cc_start: 0.6236 (mm-40) cc_final: 0.6019 (mt0) REVERT: D 119 ARG cc_start: 0.5744 (ttm170) cc_final: 0.5049 (mtm-85) REVERT: D 123 GLU cc_start: 0.6526 (mm-30) cc_final: 0.6237 (mm-30) REVERT: D 139 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6993 (mt-10) REVERT: D 257 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7510 (mmtt) REVERT: D 466 GLU cc_start: 0.6850 (mt-10) cc_final: 0.5796 (pm20) REVERT: D 483 LYS cc_start: 0.7251 (mttt) cc_final: 0.6632 (tppt) REVERT: D 494 ARG cc_start: 0.7030 (ttm110) cc_final: 0.5721 (tpm170) REVERT: D 498 ARG cc_start: 0.5882 (mmm-85) cc_final: 0.5123 (ttp80) REVERT: D 502 LYS cc_start: 0.5975 (ttmm) cc_final: 0.5317 (ttpp) REVERT: D 535 ARG cc_start: 0.6371 (mtp85) cc_final: 0.6008 (ptm160) REVERT: D 549 LYS cc_start: 0.7836 (mtpm) cc_final: 0.7021 (mttm) REVERT: D 581 SER cc_start: 0.6594 (m) cc_final: 0.6265 (p) REVERT: D 582 GLU cc_start: 0.7196 (tp30) cc_final: 0.6896 (tm-30) REVERT: D 590 ASP cc_start: 0.6492 (p0) cc_final: 0.6147 (m-30) REVERT: D 604 GLU cc_start: 0.6175 (mm-30) cc_final: 0.5512 (mm-30) REVERT: D 614 GLU cc_start: 0.7023 (tt0) cc_final: 0.5320 (mp0) REVERT: D 617 GLU cc_start: 0.6913 (tt0) cc_final: 0.6601 (tt0) REVERT: D 626 GLN cc_start: 0.6242 (mm-40) cc_final: 0.6022 (mt0) REVERT: E 152 GLN cc_start: 0.5765 (tp40) cc_final: 0.5441 (mm110) REVERT: E 194 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7287 (mm-40) REVERT: E 216 GLN cc_start: 0.6149 (mt0) cc_final: 0.5687 (mt0) REVERT: E 218 ASP cc_start: 0.7680 (m-30) cc_final: 0.6954 (OUTLIER) REVERT: E 227 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4435 (pp) REVERT: E 405 ASN cc_start: 0.7704 (m-40) cc_final: 0.7265 (m-40) REVERT: E 473 ARG cc_start: 0.6250 (mmm160) cc_final: 0.5494 (mpp-170) REVERT: E 480 GLU cc_start: 0.7110 (tt0) cc_final: 0.6591 (mp0) REVERT: E 483 LYS cc_start: 0.7867 (mttt) cc_final: 0.7196 (mmmm) REVERT: E 502 LYS cc_start: 0.5680 (mmmm) cc_final: 0.5108 (mtpt) REVERT: E 505 ASP cc_start: 0.6021 (OUTLIER) cc_final: 0.5643 (m-30) REVERT: E 535 ARG cc_start: 0.7151 (mmm160) cc_final: 0.6827 (ttp80) REVERT: E 582 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6441 (tp30) REVERT: E 603 ARG cc_start: 0.6447 (mtt180) cc_final: 0.5782 (mmp-170) REVERT: E 604 GLU cc_start: 0.6666 (mt-10) cc_final: 0.5823 (mm-30) REVERT: E 614 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7118 (tt0) REVERT: E 626 GLN cc_start: 0.7003 (mt0) cc_final: 0.6392 (mp10) REVERT: F 11 ARG cc_start: 0.2539 (OUTLIER) cc_final: 0.2170 (mtp85) REVERT: F 55 ILE cc_start: 0.3162 (OUTLIER) cc_final: 0.2836 (tt) REVERT: F 217 LYS cc_start: 0.4819 (mttt) cc_final: 0.4547 (mmtt) REVERT: F 461 LYS cc_start: 0.5329 (tptt) cc_final: 0.4966 (pptt) REVERT: F 476 GLU cc_start: 0.6445 (mt-10) cc_final: 0.5998 (tm-30) REVERT: F 483 LYS cc_start: 0.7052 (tttp) cc_final: 0.6810 (ptmm) REVERT: F 494 ARG cc_start: 0.5929 (ttp80) cc_final: 0.5394 (tpt90) REVERT: F 496 SER cc_start: 0.6885 (OUTLIER) cc_final: 0.5821 (p) REVERT: F 522 GLU cc_start: 0.6072 (pm20) cc_final: 0.5860 (pm20) REVERT: F 546 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5071 (mmm160) REVERT: F 556 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6182 (tm-30) REVERT: F 570 HIS cc_start: 0.6238 (t-90) cc_final: 0.5920 (t-170) REVERT: F 590 ASP cc_start: 0.5689 (OUTLIER) cc_final: 0.5337 (m-30) outliers start: 86 outliers final: 40 residues processed: 304 average time/residue: 1.6880 time to fit residues: 587.8684 Evaluate side-chains 282 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30230 Z= 0.185 Angle : 0.557 8.756 41025 Z= 0.296 Chirality : 0.047 0.256 4632 Planarity : 0.004 0.054 5320 Dihedral : 9.828 174.499 4162 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.47 % Favored : 93.32 % Rotamer: Outliers : 3.34 % Allowed : 15.07 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3650 helix: 0.86 (0.17), residues: 1112 sheet: 0.78 (0.22), residues: 680 loop : -1.99 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 182 HIS 0.004 0.001 HIS E 208 PHE 0.017 0.002 PHE D 445 TYR 0.018 0.001 TYR B 165 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 226 time to evaluate : 3.017 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: A 217 LYS cc_start: 0.4885 (mttt) cc_final: 0.4641 (mmtt) REVERT: A 413 ILE cc_start: 0.4601 (OUTLIER) cc_final: 0.4353 (mp) REVERT: A 461 LYS cc_start: 0.5318 (tptt) cc_final: 0.4903 (pptt) REVERT: A 476 GLU cc_start: 0.6447 (mt-10) cc_final: 0.5997 (tm-30) REVERT: A 483 LYS cc_start: 0.7147 (tttp) cc_final: 0.6879 (ptmm) REVERT: A 494 ARG cc_start: 0.5956 (ttp80) cc_final: 0.5494 (tpt90) REVERT: A 546 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.5222 (mmm160) REVERT: A 556 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6358 (tm-30) REVERT: A 570 HIS cc_start: 0.6312 (t-90) cc_final: 0.6032 (t-170) REVERT: B 152 GLN cc_start: 0.5826 (tp40) cc_final: 0.5474 (mm110) REVERT: B 216 GLN cc_start: 0.6228 (mt0) cc_final: 0.5813 (mt0) REVERT: B 218 ASP cc_start: 0.7682 (m-30) cc_final: 0.6945 (OUTLIER) REVERT: B 227 LEU cc_start: 0.4886 (OUTLIER) cc_final: 0.4354 (pp) REVERT: B 405 ASN cc_start: 0.7722 (m-40) cc_final: 0.7303 (m-40) REVERT: B 473 ARG cc_start: 0.6297 (mmm160) cc_final: 0.5540 (mpp-170) REVERT: B 480 GLU cc_start: 0.7109 (tt0) cc_final: 0.6586 (mp0) REVERT: B 483 LYS cc_start: 0.7919 (mttt) cc_final: 0.7223 (mmmm) REVERT: B 502 LYS cc_start: 0.5676 (mmmm) cc_final: 0.5103 (mtpt) REVERT: B 505 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5573 (m-30) REVERT: B 535 ARG cc_start: 0.7183 (mmm160) cc_final: 0.6800 (tmm160) REVERT: B 582 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6421 (tp30) REVERT: B 594 ASP cc_start: 0.6237 (t70) cc_final: 0.5953 (p0) REVERT: B 603 ARG cc_start: 0.6467 (mtt180) cc_final: 0.5822 (mtp85) REVERT: B 604 GLU cc_start: 0.6695 (mt-10) cc_final: 0.5851 (mm-30) REVERT: B 614 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7208 (tt0) REVERT: B 626 GLN cc_start: 0.7063 (mt0) cc_final: 0.6422 (mp10) REVERT: C 119 ARG cc_start: 0.5974 (ttm170) cc_final: 0.5168 (mtm-85) REVERT: C 123 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6216 (mm-30) REVERT: C 139 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6794 (mt-10) REVERT: C 257 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7603 (mmtt) REVERT: C 466 GLU cc_start: 0.6840 (mt-10) cc_final: 0.5764 (pm20) REVERT: C 483 LYS cc_start: 0.7247 (mttt) cc_final: 0.6601 (tppt) REVERT: C 494 ARG cc_start: 0.7027 (ttm110) cc_final: 0.5683 (tpm170) REVERT: C 498 ARG cc_start: 0.6026 (mmm-85) cc_final: 0.5247 (ttp80) REVERT: C 502 LYS cc_start: 0.6035 (ttmm) cc_final: 0.5362 (ttpp) REVERT: C 535 ARG cc_start: 0.6468 (mtp85) cc_final: 0.6049 (ptm160) REVERT: C 549 LYS cc_start: 0.7875 (mtpm) cc_final: 0.7167 (mttm) REVERT: C 581 SER cc_start: 0.6747 (m) cc_final: 0.6333 (p) REVERT: C 582 GLU cc_start: 0.7181 (tp30) cc_final: 0.6897 (tm-30) REVERT: C 590 ASP cc_start: 0.6584 (OUTLIER) cc_final: 0.6349 (m-30) REVERT: C 604 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5557 (mm-30) REVERT: C 614 GLU cc_start: 0.7099 (tt0) cc_final: 0.6596 (tt0) REVERT: C 617 GLU cc_start: 0.7017 (tt0) cc_final: 0.6679 (tt0) REVERT: C 626 GLN cc_start: 0.6249 (mm-40) cc_final: 0.6023 (mt0) REVERT: D 119 ARG cc_start: 0.5973 (ttm170) cc_final: 0.5168 (mtm-85) REVERT: D 123 GLU cc_start: 0.6517 (mm-30) cc_final: 0.6217 (mm-30) REVERT: D 139 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6821 (mt-10) REVERT: D 257 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7591 (mmtt) REVERT: D 302 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6653 (pp) REVERT: D 466 GLU cc_start: 0.6848 (mt-10) cc_final: 0.5768 (pm20) REVERT: D 483 LYS cc_start: 0.7254 (mttt) cc_final: 0.6598 (tppt) REVERT: D 494 ARG cc_start: 0.7026 (ttm110) cc_final: 0.5681 (tpm170) REVERT: D 498 ARG cc_start: 0.6022 (mmm-85) cc_final: 0.5250 (ttp80) REVERT: D 502 LYS cc_start: 0.6025 (ttmm) cc_final: 0.5358 (ttpp) REVERT: D 535 ARG cc_start: 0.6465 (mtp85) cc_final: 0.6046 (ptm160) REVERT: D 549 LYS cc_start: 0.7873 (mtpm) cc_final: 0.7166 (mttm) REVERT: D 581 SER cc_start: 0.6749 (m) cc_final: 0.6334 (p) REVERT: D 582 GLU cc_start: 0.7187 (tp30) cc_final: 0.6894 (tm-30) REVERT: D 590 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6347 (m-30) REVERT: D 604 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5571 (mm-30) REVERT: D 614 GLU cc_start: 0.7103 (tt0) cc_final: 0.6602 (tt0) REVERT: D 617 GLU cc_start: 0.7021 (tt0) cc_final: 0.6680 (tt0) REVERT: D 626 GLN cc_start: 0.6247 (mm-40) cc_final: 0.6020 (mt0) REVERT: E 103 LYS cc_start: 0.6113 (ttpt) cc_final: 0.5891 (tttm) REVERT: E 152 GLN cc_start: 0.5825 (tp40) cc_final: 0.5482 (mm110) REVERT: E 216 GLN cc_start: 0.6239 (mt0) cc_final: 0.5838 (mt0) REVERT: E 218 ASP cc_start: 0.7659 (m-30) cc_final: 0.6929 (OUTLIER) REVERT: E 227 LEU cc_start: 0.4876 (OUTLIER) cc_final: 0.4342 (pp) REVERT: E 405 ASN cc_start: 0.7728 (m-40) cc_final: 0.7309 (m-40) REVERT: E 473 ARG cc_start: 0.6275 (mmm160) cc_final: 0.5522 (mpp-170) REVERT: E 480 GLU cc_start: 0.7114 (tt0) cc_final: 0.6581 (mp0) REVERT: E 483 LYS cc_start: 0.7905 (mttt) cc_final: 0.7209 (mmmm) REVERT: E 502 LYS cc_start: 0.5684 (mmmm) cc_final: 0.5109 (mtpt) REVERT: E 505 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.5590 (m-30) REVERT: E 535 ARG cc_start: 0.7184 (mmm160) cc_final: 0.6824 (ttp80) REVERT: E 582 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6426 (tp30) REVERT: E 603 ARG cc_start: 0.6462 (mtt180) cc_final: 0.5824 (mtp85) REVERT: E 604 GLU cc_start: 0.6692 (mt-10) cc_final: 0.5851 (mm-30) REVERT: E 614 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7201 (tt0) REVERT: E 626 GLN cc_start: 0.7046 (mt0) cc_final: 0.6425 (mp10) REVERT: F 217 LYS cc_start: 0.4898 (mttt) cc_final: 0.4661 (mmtt) REVERT: F 413 ILE cc_start: 0.4615 (OUTLIER) cc_final: 0.4363 (mp) REVERT: F 461 LYS cc_start: 0.5338 (tptt) cc_final: 0.4960 (pptt) REVERT: F 476 GLU cc_start: 0.6462 (mt-10) cc_final: 0.6013 (tm-30) REVERT: F 483 LYS cc_start: 0.7157 (tttp) cc_final: 0.6896 (ptmm) REVERT: F 494 ARG cc_start: 0.5954 (ttp80) cc_final: 0.5412 (tpt90) REVERT: F 546 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5218 (mmm160) REVERT: F 556 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6235 (tm-30) REVERT: F 570 HIS cc_start: 0.6315 (t-90) cc_final: 0.5997 (t-170) REVERT: F 590 ASP cc_start: 0.5687 (OUTLIER) cc_final: 0.5376 (m-30) outliers start: 107 outliers final: 62 residues processed: 316 average time/residue: 1.6750 time to fit residues: 608.6833 Evaluate side-chains 297 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 221 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 201 optimal weight: 0.0670 chunk 258 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 352 optimal weight: 7.9990 chunk 220 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30230 Z= 0.175 Angle : 0.533 8.005 41025 Z= 0.288 Chirality : 0.046 0.257 4632 Planarity : 0.004 0.054 5320 Dihedral : 9.757 177.292 4162 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.25 % Favored : 93.53 % Rotamer: Outliers : 3.31 % Allowed : 15.42 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3650 helix: 0.86 (0.16), residues: 1112 sheet: 0.86 (0.22), residues: 670 loop : -1.97 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 182 HIS 0.003 0.001 HIS E 208 PHE 0.016 0.002 PHE D 445 TYR 0.017 0.001 TYR B 165 ARG 0.012 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 225 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.6862 (ttm170) cc_final: 0.6433 (ttm-80) REVERT: A 194 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6994 (mt0) REVERT: A 217 LYS cc_start: 0.4857 (mttt) cc_final: 0.4620 (mmtt) REVERT: A 413 ILE cc_start: 0.4583 (OUTLIER) cc_final: 0.4314 (mp) REVERT: A 461 LYS cc_start: 0.5299 (tptt) cc_final: 0.4897 (pptt) REVERT: A 476 GLU cc_start: 0.6443 (mt-10) cc_final: 0.6001 (tm-30) REVERT: A 483 LYS cc_start: 0.7140 (tttp) cc_final: 0.6869 (ptmm) REVERT: A 494 ARG cc_start: 0.5970 (ttp80) cc_final: 0.5499 (tpt90) REVERT: A 546 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.5304 (mmm160) REVERT: A 556 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6344 (tm-30) REVERT: A 570 HIS cc_start: 0.6367 (t-90) cc_final: 0.6072 (t-170) REVERT: A 590 ASP cc_start: 0.5691 (OUTLIER) cc_final: 0.5424 (m-30) REVERT: B 152 GLN cc_start: 0.5861 (tp40) cc_final: 0.5494 (mm110) REVERT: B 216 GLN cc_start: 0.6212 (mt0) cc_final: 0.5782 (mt0) REVERT: B 218 ASP cc_start: 0.7663 (m-30) cc_final: 0.6935 (OUTLIER) REVERT: B 227 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4417 (pp) REVERT: B 405 ASN cc_start: 0.7726 (m-40) cc_final: 0.7331 (m-40) REVERT: B 473 ARG cc_start: 0.6250 (mmm160) cc_final: 0.5513 (mpp-170) REVERT: B 480 GLU cc_start: 0.7110 (tt0) cc_final: 0.6591 (mp0) REVERT: B 483 LYS cc_start: 0.7919 (mttt) cc_final: 0.7203 (mmmm) REVERT: B 502 LYS cc_start: 0.5678 (mmmm) cc_final: 0.5107 (mtpt) REVERT: B 505 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5587 (m-30) REVERT: B 535 ARG cc_start: 0.7186 (mmm160) cc_final: 0.6827 (ttp80) REVERT: B 582 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6395 (tp30) REVERT: B 594 ASP cc_start: 0.6260 (t70) cc_final: 0.5987 (p0) REVERT: B 603 ARG cc_start: 0.6462 (mtt180) cc_final: 0.5803 (mtp85) REVERT: B 604 GLU cc_start: 0.6691 (mt-10) cc_final: 0.5847 (mm-30) REVERT: B 614 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7204 (tt0) REVERT: B 626 GLN cc_start: 0.7053 (mt0) cc_final: 0.6403 (mp10) REVERT: C 119 ARG cc_start: 0.5954 (ttm170) cc_final: 0.5134 (mtm-85) REVERT: C 123 GLU cc_start: 0.6531 (mm-30) cc_final: 0.6221 (mm-30) REVERT: C 139 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6746 (mt-10) REVERT: C 227 LEU cc_start: 0.6666 (mt) cc_final: 0.6297 (mp) REVERT: C 257 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7527 (mmtt) REVERT: C 466 GLU cc_start: 0.6815 (mt-10) cc_final: 0.5741 (pm20) REVERT: C 483 LYS cc_start: 0.7217 (mttt) cc_final: 0.6555 (tppt) REVERT: C 494 ARG cc_start: 0.7023 (ttm110) cc_final: 0.5686 (tpm170) REVERT: C 498 ARG cc_start: 0.6028 (mmm-85) cc_final: 0.5246 (ttp80) REVERT: C 502 LYS cc_start: 0.6034 (ttmm) cc_final: 0.5357 (ttpp) REVERT: C 535 ARG cc_start: 0.6474 (mtp85) cc_final: 0.6076 (ptm160) REVERT: C 549 LYS cc_start: 0.7872 (mtpm) cc_final: 0.7167 (mttm) REVERT: C 582 GLU cc_start: 0.7179 (tp30) cc_final: 0.6794 (mp0) REVERT: C 604 GLU cc_start: 0.6139 (mm-30) cc_final: 0.5525 (mm-30) REVERT: C 614 GLU cc_start: 0.7087 (tt0) cc_final: 0.5355 (mp0) REVERT: C 617 GLU cc_start: 0.6943 (tt0) cc_final: 0.6571 (tt0) REVERT: C 626 GLN cc_start: 0.6228 (mm-40) cc_final: 0.6004 (mt0) REVERT: D 119 ARG cc_start: 0.5957 (ttm170) cc_final: 0.5136 (mtm-85) REVERT: D 123 GLU cc_start: 0.6508 (mm-30) cc_final: 0.6199 (mm-30) REVERT: D 139 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6780 (mt-10) REVERT: D 227 LEU cc_start: 0.6674 (mt) cc_final: 0.6306 (mp) REVERT: D 257 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7517 (mmtt) REVERT: D 302 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6656 (pp) REVERT: D 466 GLU cc_start: 0.6816 (mt-10) cc_final: 0.5741 (pm20) REVERT: D 483 LYS cc_start: 0.7216 (mttt) cc_final: 0.6557 (tppt) REVERT: D 494 ARG cc_start: 0.7024 (ttm110) cc_final: 0.5690 (tpm170) REVERT: D 498 ARG cc_start: 0.6035 (mmm-85) cc_final: 0.5253 (ttp80) REVERT: D 502 LYS cc_start: 0.6034 (ttmm) cc_final: 0.5361 (ttpp) REVERT: D 535 ARG cc_start: 0.6480 (mtp85) cc_final: 0.6078 (ptm160) REVERT: D 549 LYS cc_start: 0.7870 (mtpm) cc_final: 0.7166 (mttm) REVERT: D 581 SER cc_start: 0.6763 (m) cc_final: 0.6411 (p) REVERT: D 582 GLU cc_start: 0.7178 (tp30) cc_final: 0.6738 (mp0) REVERT: D 604 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5530 (mm-30) REVERT: D 614 GLU cc_start: 0.7090 (tt0) cc_final: 0.5358 (mp0) REVERT: D 617 GLU cc_start: 0.6948 (tt0) cc_final: 0.6572 (tt0) REVERT: D 626 GLN cc_start: 0.6223 (mm-40) cc_final: 0.5998 (mt0) REVERT: E 152 GLN cc_start: 0.5851 (tp40) cc_final: 0.5486 (mm110) REVERT: E 216 GLN cc_start: 0.6227 (mt0) cc_final: 0.5871 (mt0) REVERT: E 218 ASP cc_start: 0.7651 (m-30) cc_final: 0.6913 (OUTLIER) REVERT: E 227 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4430 (pp) REVERT: E 405 ASN cc_start: 0.7727 (m-40) cc_final: 0.7331 (m-40) REVERT: E 473 ARG cc_start: 0.6248 (mmm160) cc_final: 0.5514 (mpp-170) REVERT: E 480 GLU cc_start: 0.7111 (tt0) cc_final: 0.6583 (mp0) REVERT: E 483 LYS cc_start: 0.7918 (mttt) cc_final: 0.7206 (mmmm) REVERT: E 502 LYS cc_start: 0.5687 (mmmm) cc_final: 0.5115 (mtpt) REVERT: E 505 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.5589 (m-30) REVERT: E 535 ARG cc_start: 0.7183 (mmm160) cc_final: 0.6825 (ttp80) REVERT: E 582 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6398 (tp30) REVERT: E 603 ARG cc_start: 0.6465 (mtt180) cc_final: 0.5806 (mtp85) REVERT: E 604 GLU cc_start: 0.6700 (mt-10) cc_final: 0.5857 (mm-30) REVERT: E 614 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7202 (tt0) REVERT: E 626 GLN cc_start: 0.7047 (mt0) cc_final: 0.6395 (mp10) REVERT: F 11 ARG cc_start: 0.1438 (OUTLIER) cc_final: 0.0459 (mtp180) REVERT: F 194 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6997 (mt0) REVERT: F 217 LYS cc_start: 0.4843 (mttt) cc_final: 0.4589 (mmtt) REVERT: F 413 ILE cc_start: 0.4610 (OUTLIER) cc_final: 0.4337 (mp) REVERT: F 461 LYS cc_start: 0.5310 (tptt) cc_final: 0.4941 (pptt) REVERT: F 476 GLU cc_start: 0.6449 (mt-10) cc_final: 0.6005 (tm-30) REVERT: F 483 LYS cc_start: 0.7123 (tttp) cc_final: 0.6869 (ptmm) REVERT: F 494 ARG cc_start: 0.5964 (ttp80) cc_final: 0.5422 (tpt90) REVERT: F 546 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.5306 (mmm160) REVERT: F 556 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6212 (tm-30) REVERT: F 570 HIS cc_start: 0.6353 (t-90) cc_final: 0.6047 (t-170) REVERT: F 590 ASP cc_start: 0.5713 (OUTLIER) cc_final: 0.5419 (m-30) outliers start: 106 outliers final: 66 residues processed: 317 average time/residue: 1.6360 time to fit residues: 594.9680 Evaluate side-chains 300 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 218 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 0.0770 chunk 140 optimal weight: 4.9990 chunk 210 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 224 optimal weight: 0.3980 chunk 240 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 277 optimal weight: 50.0000 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN F 305 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30230 Z= 0.146 Angle : 0.502 8.320 41025 Z= 0.271 Chirality : 0.045 0.257 4632 Planarity : 0.004 0.067 5320 Dihedral : 9.558 176.326 4162 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.25 % Favored : 93.53 % Rotamer: Outliers : 2.62 % Allowed : 16.45 % Favored : 80.93 % 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: -0.67 (0.14), residues: 3650 helix: 0.94 (0.16), residues: 1110 sheet: 0.66 (0.21), residues: 718 loop : -1.88 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 182 HIS 0.003 0.001 HIS E 208 PHE 0.012 0.001 PHE D 445 TYR 0.015 0.001 TYR B 165 ARG 0.012 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 221 time to evaluate : 3.187 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: A 110 ARG cc_start: 0.6872 (ttm170) cc_final: 0.6452 (ttm-80) REVERT: A 194 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6821 (mt0) REVERT: A 217 LYS cc_start: 0.4891 (mttt) cc_final: 0.4608 (mmtt) REVERT: A 413 ILE cc_start: 0.4522 (OUTLIER) cc_final: 0.4255 (mp) REVERT: A 461 LYS cc_start: 0.5292 (tptt) cc_final: 0.4926 (pptt) REVERT: A 476 GLU cc_start: 0.6355 (mt-10) cc_final: 0.5930 (tm-30) REVERT: A 483 LYS cc_start: 0.7088 (tttp) cc_final: 0.6818 (ptmm) REVERT: A 494 ARG cc_start: 0.5952 (ttp80) cc_final: 0.5487 (tpt90) REVERT: A 546 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5239 (mmm160) REVERT: A 556 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: A 570 HIS cc_start: 0.6346 (t-90) cc_final: 0.6077 (t-170) REVERT: B 152 GLN cc_start: 0.5852 (tp40) cc_final: 0.5479 (mm110) REVERT: B 216 GLN cc_start: 0.6125 (mt0) cc_final: 0.5736 (mt0) REVERT: B 218 ASP cc_start: 0.7654 (m-30) cc_final: 0.6923 (OUTLIER) REVERT: B 227 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4473 (pp) REVERT: B 405 ASN cc_start: 0.7714 (m-40) cc_final: 0.7293 (m-40) REVERT: B 473 ARG cc_start: 0.6198 (mmm160) cc_final: 0.5470 (mpp-170) REVERT: B 480 GLU cc_start: 0.7130 (tt0) cc_final: 0.6573 (mp0) REVERT: B 483 LYS cc_start: 0.7906 (mttt) cc_final: 0.7165 (mmmm) REVERT: B 502 LYS cc_start: 0.5668 (mmmm) cc_final: 0.5099 (mtpt) REVERT: B 505 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.5575 (m-30) REVERT: B 535 ARG cc_start: 0.7180 (mmm160) cc_final: 0.6825 (ttp80) REVERT: B 582 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6336 (tp30) REVERT: B 594 ASP cc_start: 0.6276 (t70) cc_final: 0.5979 (p0) REVERT: B 603 ARG cc_start: 0.6462 (mtt180) cc_final: 0.5771 (mtp85) REVERT: B 604 GLU cc_start: 0.6683 (mt-10) cc_final: 0.5845 (mm-30) REVERT: B 614 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7189 (tt0) REVERT: B 626 GLN cc_start: 0.6994 (mt0) cc_final: 0.6381 (mp10) REVERT: C 119 ARG cc_start: 0.5923 (ttm170) cc_final: 0.5127 (mtm-85) REVERT: C 123 GLU cc_start: 0.6487 (mm-30) cc_final: 0.6186 (mm-30) REVERT: C 139 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6737 (mt-10) REVERT: C 257 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7526 (mmtt) REVERT: C 466 GLU cc_start: 0.6852 (mt-10) cc_final: 0.5810 (pm20) REVERT: C 483 LYS cc_start: 0.7275 (mttt) cc_final: 0.6609 (tppt) REVERT: C 494 ARG cc_start: 0.7026 (ttm110) cc_final: 0.5684 (tpm170) REVERT: C 498 ARG cc_start: 0.6010 (mmm-85) cc_final: 0.5202 (ttp80) REVERT: C 502 LYS cc_start: 0.6003 (ttmm) cc_final: 0.5335 (ttpp) REVERT: C 535 ARG cc_start: 0.6469 (mtp85) cc_final: 0.6077 (ptm160) REVERT: C 549 LYS cc_start: 0.7835 (mtpm) cc_final: 0.7129 (mttm) REVERT: C 581 SER cc_start: 0.6647 (m) cc_final: 0.6315 (p) REVERT: C 582 GLU cc_start: 0.7174 (tp30) cc_final: 0.6758 (mp0) REVERT: C 604 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5479 (mm-30) REVERT: C 614 GLU cc_start: 0.7082 (tt0) cc_final: 0.5353 (mp0) REVERT: C 617 GLU cc_start: 0.6875 (tt0) cc_final: 0.6547 (tt0) REVERT: C 626 GLN cc_start: 0.6214 (mm-40) cc_final: 0.5990 (mt0) REVERT: D 119 ARG cc_start: 0.5925 (ttm170) cc_final: 0.5129 (mtm-85) REVERT: D 123 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6194 (mm-30) REVERT: D 139 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6760 (mt-10) REVERT: D 257 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7505 (mmtt) REVERT: D 302 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6674 (pp) REVERT: D 466 GLU cc_start: 0.6857 (mt-10) cc_final: 0.5814 (pm20) REVERT: D 483 LYS cc_start: 0.7281 (mttt) cc_final: 0.6606 (tppt) REVERT: D 494 ARG cc_start: 0.7014 (ttm110) cc_final: 0.5683 (tpm170) REVERT: D 498 ARG cc_start: 0.6015 (mmm-85) cc_final: 0.5206 (ttp80) REVERT: D 502 LYS cc_start: 0.6009 (ttmm) cc_final: 0.5336 (ttpp) REVERT: D 535 ARG cc_start: 0.6465 (mtp85) cc_final: 0.6075 (ptm160) REVERT: D 549 LYS cc_start: 0.7834 (mtpm) cc_final: 0.7127 (mttm) REVERT: D 581 SER cc_start: 0.6644 (m) cc_final: 0.6318 (p) REVERT: D 582 GLU cc_start: 0.7169 (tp30) cc_final: 0.6748 (mp0) REVERT: D 604 GLU cc_start: 0.6099 (mm-30) cc_final: 0.5484 (mm-30) REVERT: D 614 GLU cc_start: 0.7087 (tt0) cc_final: 0.5357 (mp0) REVERT: D 617 GLU cc_start: 0.6879 (tt0) cc_final: 0.6548 (tt0) REVERT: D 626 GLN cc_start: 0.6248 (mm-40) cc_final: 0.6021 (mt0) REVERT: E 152 GLN cc_start: 0.5854 (tp40) cc_final: 0.5484 (mm110) REVERT: E 216 GLN cc_start: 0.6124 (mt0) cc_final: 0.5734 (mt0) REVERT: E 218 ASP cc_start: 0.7642 (m-30) cc_final: 0.6904 (OUTLIER) REVERT: E 227 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4473 (pp) REVERT: E 405 ASN cc_start: 0.7713 (m-40) cc_final: 0.7292 (m-40) REVERT: E 473 ARG cc_start: 0.6206 (mmm160) cc_final: 0.5478 (mpp-170) REVERT: E 480 GLU cc_start: 0.7122 (tt0) cc_final: 0.6568 (mp0) REVERT: E 483 LYS cc_start: 0.7897 (mttt) cc_final: 0.7170 (mmmm) REVERT: E 502 LYS cc_start: 0.5683 (mmmm) cc_final: 0.5113 (mtpt) REVERT: E 505 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5579 (m-30) REVERT: E 535 ARG cc_start: 0.7175 (mmm160) cc_final: 0.6822 (ttp80) REVERT: E 582 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6343 (tp30) REVERT: E 603 ARG cc_start: 0.6469 (mtt180) cc_final: 0.5774 (mtp85) REVERT: E 604 GLU cc_start: 0.6696 (mt-10) cc_final: 0.5875 (mm-30) REVERT: E 614 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7187 (tt0) REVERT: E 626 GLN cc_start: 0.6997 (mt0) cc_final: 0.6385 (mp10) REVERT: F 194 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6823 (mt0) REVERT: F 217 LYS cc_start: 0.4891 (mttt) cc_final: 0.4608 (mmtt) REVERT: F 413 ILE cc_start: 0.4566 (OUTLIER) cc_final: 0.4297 (mp) REVERT: F 461 LYS cc_start: 0.5299 (tptt) cc_final: 0.4935 (pptt) REVERT: F 476 GLU cc_start: 0.6358 (mt-10) cc_final: 0.5928 (tm-30) REVERT: F 483 LYS cc_start: 0.7130 (tttp) cc_final: 0.6865 (ptmm) REVERT: F 494 ARG cc_start: 0.5963 (ttp80) cc_final: 0.5501 (tpt90) REVERT: F 546 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5238 (mmm160) REVERT: F 556 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6163 (tm-30) REVERT: F 570 HIS cc_start: 0.6338 (t-90) cc_final: 0.6041 (t-170) REVERT: F 590 ASP cc_start: 0.5738 (OUTLIER) cc_final: 0.5472 (m-30) outliers start: 84 outliers final: 57 residues processed: 297 average time/residue: 1.6683 time to fit residues: 568.0810 Evaluate side-chains 289 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 218 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 20.0000 chunk 337 optimal weight: 6.9990 chunk 308 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 327 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30230 Z= 0.236 Angle : 0.600 9.691 41025 Z= 0.322 Chirality : 0.048 0.254 4632 Planarity : 0.005 0.061 5320 Dihedral : 9.751 173.228 4162 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.90 % Favored : 92.88 % Rotamer: Outliers : 2.75 % Allowed : 16.45 % Favored : 80.81 % 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: -0.84 (0.14), residues: 3650 helix: 0.78 (0.16), residues: 1100 sheet: 0.76 (0.22), residues: 654 loop : -1.95 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 182 HIS 0.004 0.001 HIS E 208 PHE 0.022 0.002 PHE C 445 TYR 0.021 0.002 TYR E 165 ARG 0.005 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 211 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.6973 (ttm170) cc_final: 0.6449 (ttm-80) REVERT: A 194 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6933 (mt0) REVERT: A 413 ILE cc_start: 0.4575 (OUTLIER) cc_final: 0.4302 (mp) REVERT: A 461 LYS cc_start: 0.5272 (tptt) cc_final: 0.4892 (pptt) REVERT: A 476 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6015 (tm-30) REVERT: A 483 LYS cc_start: 0.7170 (tttp) cc_final: 0.6885 (ptmm) REVERT: A 494 ARG cc_start: 0.5976 (ttp80) cc_final: 0.5571 (tmt170) REVERT: A 546 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5264 (mmm160) REVERT: A 556 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6770 (tt0) REVERT: A 570 HIS cc_start: 0.6433 (t-90) cc_final: 0.6141 (t-170) REVERT: B 43 ASP cc_start: 0.5986 (m-30) cc_final: 0.5378 (p0) REVERT: B 103 LYS cc_start: 0.6041 (ttpt) cc_final: 0.5586 (tttm) REVERT: B 152 GLN cc_start: 0.5825 (tp40) cc_final: 0.5468 (mm110) REVERT: B 218 ASP cc_start: 0.7663 (m-30) cc_final: 0.6917 (t0) REVERT: B 227 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4366 (pp) REVERT: B 405 ASN cc_start: 0.7688 (m-40) cc_final: 0.7283 (m-40) REVERT: B 473 ARG cc_start: 0.6226 (mmm160) cc_final: 0.5485 (mpp-170) REVERT: B 480 GLU cc_start: 0.7084 (tt0) cc_final: 0.6516 (mp0) REVERT: B 483 LYS cc_start: 0.7921 (mttt) cc_final: 0.7211 (mmmm) REVERT: B 502 LYS cc_start: 0.5668 (mmmm) cc_final: 0.5091 (mtpt) REVERT: B 505 ASP cc_start: 0.5959 (OUTLIER) cc_final: 0.5582 (m-30) REVERT: B 535 ARG cc_start: 0.7180 (mmm160) cc_final: 0.6829 (ttp80) REVERT: B 582 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6353 (tp30) REVERT: B 594 ASP cc_start: 0.6319 (t70) cc_final: 0.5959 (p0) REVERT: B 603 ARG cc_start: 0.6526 (mtt180) cc_final: 0.5783 (mtp85) REVERT: B 604 GLU cc_start: 0.6704 (mt-10) cc_final: 0.5852 (mm-30) REVERT: B 614 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7231 (tt0) REVERT: B 626 GLN cc_start: 0.7081 (mt0) cc_final: 0.6398 (mp10) REVERT: C 119 ARG cc_start: 0.6144 (ttm170) cc_final: 0.5242 (mtm-85) REVERT: C 123 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6288 (mm-30) REVERT: C 139 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6700 (mt-10) REVERT: C 257 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7521 (mmtt) REVERT: C 466 GLU cc_start: 0.6853 (mt-10) cc_final: 0.5809 (pm20) REVERT: C 483 LYS cc_start: 0.7176 (mttt) cc_final: 0.6593 (mmtm) REVERT: C 494 ARG cc_start: 0.7050 (ttm110) cc_final: 0.5685 (tpm170) REVERT: C 498 ARG cc_start: 0.6252 (mmm-85) cc_final: 0.5488 (ttp80) REVERT: C 502 LYS cc_start: 0.6074 (ttmm) cc_final: 0.5388 (ttpp) REVERT: C 535 ARG cc_start: 0.6572 (mtp85) cc_final: 0.6176 (ptm160) REVERT: C 549 LYS cc_start: 0.7865 (mtpm) cc_final: 0.7165 (mttm) REVERT: C 582 GLU cc_start: 0.7184 (tp30) cc_final: 0.6822 (mp0) REVERT: C 604 GLU cc_start: 0.6061 (mm-30) cc_final: 0.5469 (mm-30) REVERT: C 614 GLU cc_start: 0.7117 (tt0) cc_final: 0.6656 (tt0) REVERT: C 617 GLU cc_start: 0.6902 (tt0) cc_final: 0.6567 (tt0) REVERT: C 626 GLN cc_start: 0.6206 (mm-40) cc_final: 0.5951 (mt0) REVERT: D 119 ARG cc_start: 0.6146 (ttm170) cc_final: 0.5243 (mtm-85) REVERT: D 123 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6291 (mm-30) REVERT: D 139 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6694 (mt-10) REVERT: D 257 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7507 (mmtt) REVERT: D 302 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6643 (pp) REVERT: D 466 GLU cc_start: 0.6848 (mt-10) cc_final: 0.5821 (pm20) REVERT: D 483 LYS cc_start: 0.7184 (mttt) cc_final: 0.6601 (mmtm) REVERT: D 494 ARG cc_start: 0.7050 (ttm110) cc_final: 0.5685 (tpm170) REVERT: D 498 ARG cc_start: 0.6253 (mmm-85) cc_final: 0.5490 (ttp80) REVERT: D 502 LYS cc_start: 0.6075 (ttmm) cc_final: 0.5389 (ttpp) REVERT: D 535 ARG cc_start: 0.6558 (mtp85) cc_final: 0.6165 (ptm160) REVERT: D 549 LYS cc_start: 0.7863 (mtpm) cc_final: 0.7162 (mttm) REVERT: D 582 GLU cc_start: 0.7172 (tp30) cc_final: 0.6789 (mp0) REVERT: D 604 GLU cc_start: 0.6068 (mm-30) cc_final: 0.5475 (mm-30) REVERT: D 614 GLU cc_start: 0.7119 (tt0) cc_final: 0.6658 (tt0) REVERT: D 617 GLU cc_start: 0.6905 (tt0) cc_final: 0.6568 (tt0) REVERT: D 626 GLN cc_start: 0.6181 (mm-40) cc_final: 0.5945 (mt0) REVERT: E 43 ASP cc_start: 0.5980 (m-30) cc_final: 0.5424 (p0) REVERT: E 103 LYS cc_start: 0.6049 (ttpt) cc_final: 0.5582 (tttm) REVERT: E 152 GLN cc_start: 0.5833 (tp40) cc_final: 0.5452 (mm110) REVERT: E 218 ASP cc_start: 0.7648 (m-30) cc_final: 0.6901 (t0) REVERT: E 227 LEU cc_start: 0.4921 (OUTLIER) cc_final: 0.4365 (pp) REVERT: E 405 ASN cc_start: 0.7688 (m-40) cc_final: 0.7283 (m-40) REVERT: E 473 ARG cc_start: 0.6227 (mmm160) cc_final: 0.5488 (mpp-170) REVERT: E 480 GLU cc_start: 0.7142 (tt0) cc_final: 0.6585 (mp0) REVERT: E 483 LYS cc_start: 0.7925 (mttt) cc_final: 0.7214 (mmmm) REVERT: E 502 LYS cc_start: 0.5672 (mmmm) cc_final: 0.5093 (mtpt) REVERT: E 505 ASP cc_start: 0.5960 (OUTLIER) cc_final: 0.5584 (m-30) REVERT: E 535 ARG cc_start: 0.7174 (mmm160) cc_final: 0.6831 (ttp80) REVERT: E 582 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6359 (tp30) REVERT: E 603 ARG cc_start: 0.6556 (mtt180) cc_final: 0.5807 (mtp85) REVERT: E 604 GLU cc_start: 0.6712 (mt-10) cc_final: 0.5881 (mm-30) REVERT: E 614 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7205 (tt0) REVERT: E 626 GLN cc_start: 0.7083 (mt0) cc_final: 0.6400 (mp10) REVERT: F 194 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6916 (mt0) REVERT: F 413 ILE cc_start: 0.4586 (OUTLIER) cc_final: 0.4307 (mp) REVERT: F 461 LYS cc_start: 0.5251 (tptt) cc_final: 0.4904 (pptt) REVERT: F 476 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6014 (tm-30) REVERT: F 483 LYS cc_start: 0.7166 (tttp) cc_final: 0.6903 (ptmm) REVERT: F 494 ARG cc_start: 0.5964 (ttp80) cc_final: 0.5517 (tmt170) REVERT: F 546 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5254 (mmm160) REVERT: F 556 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6298 (tm-30) REVERT: F 570 HIS cc_start: 0.6434 (t-90) cc_final: 0.6114 (t-170) REVERT: F 590 ASP cc_start: 0.5790 (OUTLIER) cc_final: 0.5537 (m-30) outliers start: 88 outliers final: 57 residues processed: 286 average time/residue: 1.7033 time to fit residues: 556.3776 Evaluate side-chains 276 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 203 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 20.0000 chunk 347 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 164 optimal weight: 0.3980 chunk 241 optimal weight: 2.9990 chunk 364 optimal weight: 30.0000 chunk 335 optimal weight: 5.9990 chunk 290 optimal weight: 0.4980 chunk 30 optimal weight: 20.0000 chunk 224 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30230 Z= 0.231 Angle : 0.590 11.042 41025 Z= 0.317 Chirality : 0.048 0.252 4632 Planarity : 0.005 0.060 5320 Dihedral : 9.630 170.684 4158 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.74 % Favored : 93.04 % Rotamer: Outliers : 2.37 % Allowed : 16.89 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3650 helix: 0.67 (0.16), residues: 1106 sheet: 0.82 (0.22), residues: 630 loop : -2.05 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 182 HIS 0.004 0.001 HIS E 459 PHE 0.021 0.002 PHE C 445 TYR 0.019 0.002 TYR D 628 ARG 0.005 0.000 ARG F 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 209 time to evaluate : 3.043 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: A 110 ARG cc_start: 0.6903 (ttm170) cc_final: 0.6363 (ttm-80) REVERT: A 194 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6915 (mt0) REVERT: A 315 ARG cc_start: 0.5522 (mmt180) cc_final: 0.5274 (mmt-90) REVERT: A 322 ARG cc_start: 0.4856 (mtt180) cc_final: 0.4524 (mpp80) REVERT: A 461 LYS cc_start: 0.5234 (tptt) cc_final: 0.4888 (pptt) REVERT: A 476 GLU cc_start: 0.6350 (mt-10) cc_final: 0.5900 (tm-30) REVERT: A 483 LYS cc_start: 0.7156 (tttp) cc_final: 0.6891 (ptmm) REVERT: A 494 ARG cc_start: 0.5954 (ttp80) cc_final: 0.5583 (tmt170) REVERT: A 546 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5311 (mmm160) REVERT: A 556 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: A 570 HIS cc_start: 0.6480 (t-90) cc_final: 0.6164 (t-170) REVERT: B 152 GLN cc_start: 0.5846 (tp40) cc_final: 0.5467 (mm110) REVERT: B 218 ASP cc_start: 0.7659 (m-30) cc_final: 0.6905 (t0) REVERT: B 227 LEU cc_start: 0.4874 (OUTLIER) cc_final: 0.4390 (pp) REVERT: B 405 ASN cc_start: 0.7687 (m-40) cc_final: 0.7279 (m-40) REVERT: B 473 ARG cc_start: 0.6227 (mmm160) cc_final: 0.5516 (mmp80) REVERT: B 480 GLU cc_start: 0.7127 (tt0) cc_final: 0.6549 (mp0) REVERT: B 483 LYS cc_start: 0.7935 (mttt) cc_final: 0.7191 (mmmm) REVERT: B 502 LYS cc_start: 0.5698 (mmmm) cc_final: 0.5091 (mtpt) REVERT: B 505 ASP cc_start: 0.5964 (OUTLIER) cc_final: 0.5587 (m-30) REVERT: B 535 ARG cc_start: 0.7193 (mmm160) cc_final: 0.6850 (ttp80) REVERT: B 582 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6406 (tp30) REVERT: B 594 ASP cc_start: 0.6392 (t70) cc_final: 0.5998 (p0) REVERT: B 603 ARG cc_start: 0.6559 (mtt180) cc_final: 0.5722 (mmp-170) REVERT: B 604 GLU cc_start: 0.6714 (mt-10) cc_final: 0.5898 (mm-30) REVERT: B 614 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7202 (tt0) REVERT: B 626 GLN cc_start: 0.7072 (mt0) cc_final: 0.6439 (mp10) REVERT: C 119 ARG cc_start: 0.6110 (ttm170) cc_final: 0.5168 (mtm-85) REVERT: C 123 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6303 (mm-30) REVERT: C 139 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6713 (mt-10) REVERT: C 257 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7465 (mmtt) REVERT: C 466 GLU cc_start: 0.6889 (mt-10) cc_final: 0.5806 (pm20) REVERT: C 483 LYS cc_start: 0.7190 (mttt) cc_final: 0.6604 (mmtm) REVERT: C 494 ARG cc_start: 0.7056 (ttm110) cc_final: 0.5708 (tpm170) REVERT: C 498 ARG cc_start: 0.6217 (mmm-85) cc_final: 0.5433 (ttp80) REVERT: C 502 LYS cc_start: 0.6062 (ttmm) cc_final: 0.5390 (ttpp) REVERT: C 535 ARG cc_start: 0.6615 (mtp85) cc_final: 0.6225 (ptm160) REVERT: C 549 LYS cc_start: 0.7846 (mtpm) cc_final: 0.7137 (mttm) REVERT: C 582 GLU cc_start: 0.7167 (tp30) cc_final: 0.6820 (mp0) REVERT: C 604 GLU cc_start: 0.6005 (mm-30) cc_final: 0.5420 (mm-30) REVERT: C 614 GLU cc_start: 0.7120 (tt0) cc_final: 0.5381 (mp0) REVERT: C 617 GLU cc_start: 0.6858 (tt0) cc_final: 0.6508 (tt0) REVERT: C 626 GLN cc_start: 0.6183 (mm-40) cc_final: 0.5936 (mt0) REVERT: D 119 ARG cc_start: 0.6117 (ttm170) cc_final: 0.5166 (mtm-85) REVERT: D 123 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6304 (mm-30) REVERT: D 139 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6723 (mt-10) REVERT: D 257 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7455 (mmtt) REVERT: D 302 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6581 (pp) REVERT: D 466 GLU cc_start: 0.6881 (mt-10) cc_final: 0.5805 (pm20) REVERT: D 483 LYS cc_start: 0.7189 (mttt) cc_final: 0.6604 (mmtm) REVERT: D 494 ARG cc_start: 0.7056 (ttm110) cc_final: 0.5706 (tpm170) REVERT: D 498 ARG cc_start: 0.6214 (mmm-85) cc_final: 0.5434 (ttp80) REVERT: D 502 LYS cc_start: 0.6070 (ttmm) cc_final: 0.5401 (ttpp) REVERT: D 535 ARG cc_start: 0.6612 (mtp85) cc_final: 0.6223 (ptm160) REVERT: D 549 LYS cc_start: 0.7844 (mtpm) cc_final: 0.7133 (mttm) REVERT: D 582 GLU cc_start: 0.7148 (tp30) cc_final: 0.6791 (mp0) REVERT: D 604 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5428 (mm-30) REVERT: D 614 GLU cc_start: 0.7128 (tt0) cc_final: 0.6664 (tt0) REVERT: D 617 GLU cc_start: 0.6853 (tt0) cc_final: 0.6505 (tt0) REVERT: D 626 GLN cc_start: 0.6180 (mm-40) cc_final: 0.5936 (mt0) REVERT: E 43 ASP cc_start: 0.5952 (m-30) cc_final: 0.5390 (p0) REVERT: E 152 GLN cc_start: 0.5835 (tp40) cc_final: 0.5459 (mm110) REVERT: E 218 ASP cc_start: 0.7672 (m-30) cc_final: 0.6913 (OUTLIER) REVERT: E 227 LEU cc_start: 0.4870 (OUTLIER) cc_final: 0.4387 (pp) REVERT: E 405 ASN cc_start: 0.7684 (m-40) cc_final: 0.7271 (m-40) REVERT: E 473 ARG cc_start: 0.6225 (mmm160) cc_final: 0.5514 (mmp80) REVERT: E 480 GLU cc_start: 0.7128 (tt0) cc_final: 0.6550 (mp0) REVERT: E 483 LYS cc_start: 0.7934 (mttt) cc_final: 0.7191 (mmmm) REVERT: E 502 LYS cc_start: 0.5701 (mmmm) cc_final: 0.5094 (mtpt) REVERT: E 505 ASP cc_start: 0.5960 (OUTLIER) cc_final: 0.5583 (m-30) REVERT: E 535 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6869 (ttp80) REVERT: E 582 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6400 (tp30) REVERT: E 603 ARG cc_start: 0.6543 (mtt180) cc_final: 0.5711 (mmp-170) REVERT: E 604 GLU cc_start: 0.6688 (mt-10) cc_final: 0.5871 (mm-30) REVERT: E 614 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7201 (tt0) REVERT: E 626 GLN cc_start: 0.7089 (mt0) cc_final: 0.6456 (mp10) REVERT: F 194 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6916 (mt0) REVERT: F 322 ARG cc_start: 0.4869 (mtt180) cc_final: 0.4531 (mpp80) REVERT: F 413 ILE cc_start: 0.4584 (OUTLIER) cc_final: 0.4290 (mp) REVERT: F 461 LYS cc_start: 0.5281 (tptt) cc_final: 0.4886 (pptt) REVERT: F 476 GLU cc_start: 0.6401 (mt-10) cc_final: 0.5948 (tm-30) REVERT: F 483 LYS cc_start: 0.7186 (tttp) cc_final: 0.6955 (ptmm) REVERT: F 494 ARG cc_start: 0.5979 (ttp80) cc_final: 0.5611 (tmt170) REVERT: F 546 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5303 (mmm160) REVERT: F 556 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6251 (tm-30) REVERT: F 570 HIS cc_start: 0.6496 (t-90) cc_final: 0.6151 (t-170) outliers start: 76 outliers final: 55 residues processed: 272 average time/residue: 1.6948 time to fit residues: 528.5975 Evaluate side-chains 269 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 201 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 3.9990 chunk 309 optimal weight: 0.0570 chunk 88 optimal weight: 0.5980 chunk 267 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 80 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS F 305 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.223939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.162914 restraints weight = 30992.377| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.17 r_work: 0.3639 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30230 Z= 0.144 Angle : 0.506 8.747 41025 Z= 0.273 Chirality : 0.045 0.252 4632 Planarity : 0.004 0.053 5320 Dihedral : 9.393 174.380 4158 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.95 % Favored : 93.84 % Rotamer: Outliers : 2.00 % Allowed : 17.23 % Favored : 80.77 % 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: -0.74 (0.14), residues: 3650 helix: 0.90 (0.17), residues: 1106 sheet: 0.66 (0.22), residues: 680 loop : -1.90 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 182 HIS 0.002 0.001 HIS B 208 PHE 0.012 0.001 PHE D 445 TYR 0.015 0.001 TYR E 165 ARG 0.006 0.000 ARG F 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10710.83 seconds wall clock time: 190 minutes 33.34 seconds (11433.34 seconds total)