Starting phenix.real_space_refine on Sun Feb 18 20:53:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/02_2024/6nm9_9398.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/02_2024/6nm9_9398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/02_2024/6nm9_9398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/02_2024/6nm9_9398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/02_2024/6nm9_9398.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/02_2024/6nm9_9398.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 50 5.49 5 Mg 4 5.21 5 S 70 5.16 5 C 14536 2.51 5 N 3778 2.21 5 O 4478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "B GLU 5": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B ARG 737": "NH1" <-> "NH2" Residue "B ARG 747": "NH1" <-> "NH2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B ARG 883": "NH1" <-> "NH2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B GLU 916": "OE1" <-> "OE2" Residue "B GLU 1097": "OE1" <-> "OE2" Residue "B GLU 1117": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "D GLU 5": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 382": "OE1" <-> "OE2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D GLU 484": "OE1" <-> "OE2" Residue "D ARG 548": "NH1" <-> "NH2" Residue "D GLU 610": "OE1" <-> "OE2" Residue "D GLU 659": "OE1" <-> "OE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D ARG 737": "NH1" <-> "NH2" Residue "D ARG 747": "NH1" <-> "NH2" Residue "D GLU 755": "OE1" <-> "OE2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 887": "NH1" <-> "NH2" Residue "D GLU 916": "OE1" <-> "OE2" Residue "D GLU 1097": "OE1" <-> "OE2" Residue "D GLU 1117": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22916 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 951 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "B" Number of atoms: 9970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9970 Classifications: {'peptide': 1205} Link IDs: {'PTRANS': 25, 'TRANS': 1179} Chain breaks: 5 Chain: "G" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "C" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 951 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "D" Number of atoms: 9970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9970 Classifications: {'peptide': 1205} Link IDs: {'PTRANS': 25, 'TRANS': 1179} Chain breaks: 5 Chain: "E" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.69, per 1000 atoms: 0.55 Number of scatterers: 22916 At special positions: 0 Unit cell: (175.89, 169.494, 110.864, 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 70 16.00 P 50 15.00 Mg 4 11.99 O 4478 8.00 N 3778 7.00 C 14536 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: 10.12 Conformation dependent library (CDL) restraints added in 3.9 seconds 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5060 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 24 sheets defined 47.8% alpha, 7.3% beta 8 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 7.14 Creating SS restraints... Processing helix chain 'A' and resid 127 through 148 removed outlier: 4.359A pdb=" N ILE A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.791A pdb=" N ARG A 203 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 46 through 67 Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.519A pdb=" N TYR B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 4.120A pdb=" N ALA B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 109 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.019A pdb=" N VAL B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 151 through 160 removed outlier: 4.064A pdb=" N ASN B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.510A pdb=" N ARG B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.931A pdb=" N VAL B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 removed outlier: 4.284A pdb=" N PHE B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 221' Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.594A pdb=" N PHE B 225 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 229 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 341 through 352 removed outlier: 4.009A pdb=" N SER B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 371 removed outlier: 3.556A pdb=" N ASP B 360 " --> pdb=" O ASN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 409 through 437 removed outlier: 5.745A pdb=" N LYS B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 471 removed outlier: 4.564A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.221A pdb=" N ASP B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 512 removed outlier: 4.213A pdb=" N HIS B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 588 through 598 Proline residue: B 594 - end of helix Processing helix chain 'B' and resid 610 through 619 Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.661A pdb=" N LEU B 635 " --> pdb=" O ASP B 631 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 811 through 823 removed outlier: 3.819A pdb=" N GLU B 815 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 817 " --> pdb=" O ASN B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 884 removed outlier: 3.603A pdb=" N LEU B 876 " --> pdb=" O TYR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 removed outlier: 3.684A pdb=" N LYS B 897 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 901 " --> pdb=" O LYS B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 913 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 927 through 930 removed outlier: 3.548A pdb=" N GLY B 930 " --> pdb=" O LEU B 927 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 927 through 930' Processing helix chain 'B' and resid 939 through 955 removed outlier: 3.761A pdb=" N LYS B 953 " --> pdb=" O MET B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 986 removed outlier: 3.740A pdb=" N MET B 986 " --> pdb=" O PHE B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1030 Processing helix chain 'B' and resid 1091 through 1101 Processing helix chain 'B' and resid 1111 through 1116 Processing helix chain 'B' and resid 1120 through 1135 removed outlier: 3.732A pdb=" N TYR B1124 " --> pdb=" O ASP B1120 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B1125 " --> pdb=" O LYS B1121 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER B1126 " --> pdb=" O ALA B1122 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B1130 " --> pdb=" O SER B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1169 removed outlier: 4.683A pdb=" N ALA B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1199 Processing helix chain 'B' and resid 1214 through 1225 Processing helix chain 'C' and resid 127 through 148 removed outlier: 4.359A pdb=" N ILE C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.792A pdb=" N ARG C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 37 through 46 Processing helix chain 'D' and resid 46 through 67 Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.520A pdb=" N TYR D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER D 79 " --> pdb=" O ASN D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 112 removed outlier: 4.119A pdb=" N ALA D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 126 through 131 Processing helix chain 'D' and resid 134 through 142 removed outlier: 4.020A pdb=" N VAL D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 151 through 160 removed outlier: 4.064A pdb=" N ASN D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.510A pdb=" N ARG D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 198 through 208 removed outlier: 3.930A pdb=" N VAL D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU D 204 " --> pdb=" O HIS D 200 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 removed outlier: 4.284A pdb=" N PHE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 221' Processing helix chain 'D' and resid 222 through 230 removed outlier: 3.594A pdb=" N PHE D 225 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 229 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 263 through 266 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 341 through 352 removed outlier: 4.009A pdb=" N SER D 345 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR D 346 " --> pdb=" O PRO D 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 371 removed outlier: 3.555A pdb=" N ASP D 360 " --> pdb=" O ASN D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 392 Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 409 through 437 removed outlier: 5.746A pdb=" N LYS D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 471 removed outlier: 4.563A pdb=" N MET D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 498 removed outlier: 4.221A pdb=" N ASP D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 512 removed outlier: 4.213A pdb=" N HIS D 502 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR D 510 " --> pdb=" O ALA D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 588 through 598 Proline residue: D 594 - end of helix Processing helix chain 'D' and resid 610 through 619 Processing helix chain 'D' and resid 630 through 646 removed outlier: 3.660A pdb=" N LEU D 635 " --> pdb=" O ASP D 631 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 676 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 786 through 790 Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.819A pdb=" N GLU D 815 " --> pdb=" O LYS D 811 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 817 " --> pdb=" O ASN D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 884 removed outlier: 3.603A pdb=" N LEU D 876 " --> pdb=" O TYR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 901 removed outlier: 3.684A pdb=" N LYS D 897 " --> pdb=" O ILE D 893 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 901 " --> pdb=" O LYS D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 913 Processing helix chain 'D' and resid 913 through 919 Processing helix chain 'D' and resid 927 through 930 removed outlier: 3.549A pdb=" N GLY D 930 " --> pdb=" O LEU D 927 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 927 through 930' Processing helix chain 'D' and resid 939 through 955 removed outlier: 3.760A pdb=" N LYS D 953 " --> pdb=" O MET D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 986 removed outlier: 3.741A pdb=" N MET D 986 " --> pdb=" O PHE D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1020 through 1030 Processing helix chain 'D' and resid 1091 through 1101 Processing helix chain 'D' and resid 1111 through 1116 Processing helix chain 'D' and resid 1120 through 1135 removed outlier: 3.732A pdb=" N TYR D1124 " --> pdb=" O ASP D1120 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER D1125 " --> pdb=" O LYS D1121 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER D1126 " --> pdb=" O ALA D1122 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D1130 " --> pdb=" O SER D1126 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1169 removed outlier: 4.683A pdb=" N ALA D1169 " --> pdb=" O ARG D1165 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1199 Processing helix chain 'D' and resid 1214 through 1225 Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA2, first strand: chain 'B' and resid 521 through 522 removed outlier: 3.651A pdb=" N ARG B 747 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 793 " --> pdb=" O ARG B 747 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR B 794 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR B 553 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 552 " --> pdb=" O TYR B 549 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 554 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.932A pdb=" N ARG B 737 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 757 through 759 removed outlier: 4.696A pdb=" N VAL B 757 " --> pdb=" O LYS B 785 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B 759 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 783 " --> pdb=" O HIS B 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AA7, first strand: chain 'B' and resid 850 through 855 removed outlier: 4.510A pdb=" N GLU B 925 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 922 " --> pdb=" O PHE B 994 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 996 " --> pdb=" O ILE B 922 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU B 924 " --> pdb=" O ILE B 996 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 858 through 863 removed outlier: 3.598A pdb=" N ILE B 859 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 863 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1033 through 1037 removed outlier: 3.869A pdb=" N ARG B1033 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B1035 " --> pdb=" O GLU B1044 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id=AB2, first strand: chain 'B' and resid 1139 through 1140 Processing sheet with id=AB3, first strand: chain 'B' and resid 1151 through 1152 removed outlier: 3.941A pdb=" N TYR B1162 " --> pdb=" O SER B1152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AB5, first strand: chain 'D' and resid 521 through 522 removed outlier: 3.651A pdb=" N ARG D 747 " --> pdb=" O GLN D 793 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 793 " --> pdb=" O ARG D 747 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR D 794 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR D 553 " --> pdb=" O ILE D 704 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 552 " --> pdb=" O TYR D 549 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 554 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 339 Processing sheet with id=AB7, first strand: chain 'D' and resid 736 through 737 removed outlier: 3.931A pdb=" N ARG D 737 " --> pdb=" O ALA D 801 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 757 through 759 removed outlier: 4.685A pdb=" N VAL D 757 " --> pdb=" O LYS D 785 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS D 759 " --> pdb=" O VAL D 783 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 783 " --> pdb=" O HIS D 759 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 765 through 766 Processing sheet with id=AC1, first strand: chain 'D' and resid 850 through 855 removed outlier: 4.508A pdb=" N GLU D 925 " --> pdb=" O ILE D 831 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 922 " --> pdb=" O PHE D 994 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE D 996 " --> pdb=" O ILE D 922 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU D 924 " --> pdb=" O ILE D 996 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 858 through 863 removed outlier: 3.598A pdb=" N ILE D 859 " --> pdb=" O THR D 870 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 863 " --> pdb=" O ILE D 866 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1033 through 1037 removed outlier: 3.868A pdb=" N ARG D1033 " --> pdb=" O ALA D1046 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D1035 " --> pdb=" O GLU D1044 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1070 through 1072 Processing sheet with id=AC5, first strand: chain 'D' and resid 1139 through 1140 Processing sheet with id=AC6, first strand: chain 'D' and resid 1151 through 1152 removed outlier: 3.941A pdb=" N TYR D1162 " --> pdb=" O SER D1152 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 7.91 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4818 1.33 - 1.45: 5609 1.45 - 1.57: 12847 1.57 - 1.69: 98 1.69 - 1.81: 116 Bond restraints: 23488 Sorted by residual: bond pdb=" CA ALA D 901 " pdb=" C ALA D 901 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.80e-02 3.09e+03 1.14e+01 bond pdb=" CA ALA B 901 " pdb=" C ALA B 901 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.80e-02 3.09e+03 1.14e+01 bond pdb=" N ASP D 572 " pdb=" CA ASP D 572 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.32e-02 5.74e+03 8.64e+00 bond pdb=" N ASP B 572 " pdb=" CA ASP B 572 " ideal model delta sigma weight residual 1.459 1.497 -0.039 1.32e-02 5.74e+03 8.60e+00 bond pdb=" CA CYS D 912 " pdb=" C CYS D 912 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.80e-02 3.09e+03 7.80e+00 ... (remaining 23483 not shown) Histogram of bond angle deviations from ideal: 98.98 - 105.99: 546 105.99 - 113.00: 12387 113.00 - 120.01: 8763 120.01 - 127.02: 9852 127.02 - 134.03: 270 Bond angle restraints: 31818 Sorted by residual: angle pdb=" N VAL B 216 " pdb=" CA VAL B 216 " pdb=" C VAL B 216 " ideal model delta sigma weight residual 113.71 108.02 5.69 9.50e-01 1.11e+00 3.59e+01 angle pdb=" N VAL D 216 " pdb=" CA VAL D 216 " pdb=" C VAL D 216 " ideal model delta sigma weight residual 113.71 108.02 5.69 9.50e-01 1.11e+00 3.59e+01 angle pdb=" C THR B 85 " pdb=" N ARG B 86 " pdb=" CA ARG B 86 " ideal model delta sigma weight residual 122.68 115.72 6.96 1.47e+00 4.63e-01 2.24e+01 angle pdb=" N ILE C 214 " pdb=" CA ILE C 214 " pdb=" C ILE C 214 " ideal model delta sigma weight residual 112.98 107.27 5.71 1.25e+00 6.40e-01 2.09e+01 angle pdb=" N ILE A 214 " pdb=" CA ILE A 214 " pdb=" C ILE A 214 " ideal model delta sigma weight residual 112.98 107.28 5.70 1.25e+00 6.40e-01 2.08e+01 ... (remaining 31813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 13829 33.06 - 66.12: 409 66.12 - 99.19: 40 99.19 - 132.25: 0 132.25 - 165.31: 2 Dihedral angle restraints: 14280 sinusoidal: 6436 harmonic: 7844 Sorted by residual: dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual -128.00 37.31 -165.31 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" O4' U E 16 " pdb=" C1' U E 16 " pdb=" N1 U E 16 " pdb=" C2 U E 16 " ideal model delta sinusoidal sigma weight residual -128.00 37.25 -165.25 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" CA TYR B 214 " pdb=" C TYR B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta harmonic sigma weight residual -180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 14277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3198 0.087 - 0.174: 226 0.174 - 0.261: 8 0.261 - 0.347: 2 0.347 - 0.434: 2 Chirality restraints: 3436 Sorted by residual: chirality pdb=" CA ASP D 572 " pdb=" N ASP D 572 " pdb=" C ASP D 572 " pdb=" CB ASP D 572 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA ASP B 572 " pdb=" N ASP B 572 " pdb=" C ASP B 572 " pdb=" CB ASP B 572 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C1' C G 11 " pdb=" O4' C G 11 " pdb=" C2' C G 11 " pdb=" N1 C G 11 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3433 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 24 " 0.056 2.00e-02 2.50e+03 2.38e-02 1.71e+01 pdb=" N9 G G 24 " -0.055 2.00e-02 2.50e+03 pdb=" C8 G G 24 " -0.009 2.00e-02 2.50e+03 pdb=" N7 G G 24 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G G 24 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G G 24 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G G 24 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G G 24 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G G 24 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G G 24 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G G 24 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G G 24 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G E 24 " 0.056 2.00e-02 2.50e+03 2.36e-02 1.68e+01 pdb=" N9 G E 24 " -0.055 2.00e-02 2.50e+03 pdb=" C8 G E 24 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G E 24 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G E 24 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G E 24 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G E 24 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G E 24 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G E 24 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G E 24 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G E 24 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G E 24 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 25 " 0.039 2.00e-02 2.50e+03 1.78e-02 8.75e+00 pdb=" N9 A E 25 " -0.041 2.00e-02 2.50e+03 pdb=" C8 A E 25 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A E 25 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A E 25 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A E 25 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A E 25 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A E 25 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A E 25 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A E 25 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A E 25 " -0.001 2.00e-02 2.50e+03 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 249 2.49 - 3.09: 18079 3.09 - 3.69: 35646 3.69 - 4.30: 51424 4.30 - 4.90: 81806 Nonbonded interactions: 187204 Sorted by model distance: nonbonded pdb=" OP2 A G 19 " pdb="MG MG B1301 " model vdw 1.884 2.170 nonbonded pdb=" NZ LYS A 202 " pdb="MG MG A 301 " model vdw 1.991 2.250 nonbonded pdb=" OP2 A E 19 " pdb="MG MG D1301 " model vdw 2.101 2.170 nonbonded pdb=" NZ LYS C 202 " pdb="MG MG C 301 " model vdw 2.122 2.250 nonbonded pdb=" NH1 ARG D 18 " pdb=" O5' G E 24 " model vdw 2.196 2.520 ... (remaining 187199 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 4.410 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 65.490 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.008 0.061 23488 Z= 0.479 Angle : 0.771 9.444 31818 Z= 0.449 Chirality : 0.049 0.434 3436 Planarity : 0.004 0.049 3876 Dihedral : 16.063 165.309 9220 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.60 % Favored : 87.33 % Rotamer: Outliers : 0.29 % Allowed : 8.10 % Favored : 91.60 % Cbeta Deviations : 0.12 % 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: -4.62 (0.13), residues: 2612 helix: -2.53 (0.12), residues: 1142 sheet: -2.86 (0.32), residues: 234 loop : -3.66 (0.15), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 534 HIS 0.005 0.001 HIS D 733 PHE 0.021 0.002 PHE B 61 TYR 0.032 0.002 TYR A 188 ARG 0.009 0.001 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 451 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.8892 (m-40) cc_final: 0.8589 (t0) REVERT: A 148 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8281 (ttmm) REVERT: A 174 GLU cc_start: 0.8392 (tt0) cc_final: 0.8092 (tt0) REVERT: A 219 GLU cc_start: 0.8453 (pt0) cc_final: 0.7794 (pm20) REVERT: A 231 ASN cc_start: 0.8264 (t0) cc_final: 0.8046 (t0) REVERT: B 1 MET cc_start: 0.5935 (ttt) cc_final: 0.5199 (ttt) REVERT: B 5 GLU cc_start: 0.8366 (tt0) cc_final: 0.7937 (tt0) REVERT: B 174 ARG cc_start: 0.8350 (tpp80) cc_final: 0.8080 (ttm-80) REVERT: B 179 ASN cc_start: 0.7453 (m110) cc_final: 0.7217 (m110) REVERT: B 219 PHE cc_start: 0.7861 (m-80) cc_final: 0.7587 (m-80) REVERT: B 456 MET cc_start: 0.7715 (mtt) cc_final: 0.7363 (mtp) REVERT: B 496 ILE cc_start: 0.8619 (mm) cc_final: 0.8329 (mm) REVERT: B 514 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7745 (mtmm) REVERT: B 522 LYS cc_start: 0.8833 (tttt) cc_final: 0.8457 (tttm) REVERT: B 525 PHE cc_start: 0.8675 (m-10) cc_final: 0.8441 (m-10) REVERT: B 527 ASN cc_start: 0.8485 (t0) cc_final: 0.8123 (t0) REVERT: B 531 MET cc_start: 0.8048 (ttm) cc_final: 0.7580 (ttm) REVERT: B 701 MET cc_start: 0.7584 (tmm) cc_final: 0.7341 (tmm) REVERT: B 754 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8036 (mp0) REVERT: B 852 GLU cc_start: 0.7383 (tp30) cc_final: 0.7012 (tp30) REVERT: B 882 GLU cc_start: 0.8100 (tp30) cc_final: 0.7597 (tt0) REVERT: B 986 MET cc_start: 0.8461 (mtt) cc_final: 0.8058 (mmm) REVERT: B 1027 PHE cc_start: 0.8532 (t80) cc_final: 0.8112 (t80) REVERT: B 1137 MET cc_start: 0.8963 (mtp) cc_final: 0.8619 (mtp) REVERT: C 148 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8259 (ttmm) REVERT: C 174 GLU cc_start: 0.8420 (tt0) cc_final: 0.8124 (tt0) REVERT: C 219 GLU cc_start: 0.8449 (pt0) cc_final: 0.7524 (pm20) REVERT: C 231 ASN cc_start: 0.8252 (t0) cc_final: 0.8018 (t0) REVERT: D 1 MET cc_start: 0.5927 (ttt) cc_final: 0.5190 (ttt) REVERT: D 5 GLU cc_start: 0.8367 (tt0) cc_final: 0.7937 (tt0) REVERT: D 88 GLU cc_start: 0.4525 (OUTLIER) cc_final: 0.4317 (pp20) REVERT: D 174 ARG cc_start: 0.8353 (tpp80) cc_final: 0.8082 (ttm-80) REVERT: D 179 ASN cc_start: 0.7442 (m110) cc_final: 0.7207 (m110) REVERT: D 456 MET cc_start: 0.7711 (mtt) cc_final: 0.7356 (mtp) REVERT: D 496 ILE cc_start: 0.8621 (mm) cc_final: 0.8338 (mm) REVERT: D 514 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7724 (mtmm) REVERT: D 522 LYS cc_start: 0.8822 (tttt) cc_final: 0.8446 (tttm) REVERT: D 525 PHE cc_start: 0.8675 (m-10) cc_final: 0.8443 (m-10) REVERT: D 527 ASN cc_start: 0.8487 (t0) cc_final: 0.8122 (t0) REVERT: D 531 MET cc_start: 0.8038 (ttm) cc_final: 0.7562 (ttm) REVERT: D 701 MET cc_start: 0.7586 (tmm) cc_final: 0.7343 (tmm) REVERT: D 754 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8164 (mp0) REVERT: D 786 ASP cc_start: 0.8863 (m-30) cc_final: 0.8631 (m-30) REVERT: D 852 GLU cc_start: 0.7370 (tp30) cc_final: 0.6995 (tp30) REVERT: D 882 GLU cc_start: 0.8108 (tp30) cc_final: 0.7602 (tt0) REVERT: D 986 MET cc_start: 0.8464 (mtt) cc_final: 0.8058 (mmm) REVERT: D 1027 PHE cc_start: 0.8534 (t80) cc_final: 0.8112 (t80) REVERT: D 1137 MET cc_start: 0.8996 (mtp) cc_final: 0.8689 (mtp) outliers start: 7 outliers final: 2 residues processed: 458 average time/residue: 0.4210 time to fit residues: 281.9367 Evaluate side-chains 332 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 329 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.9990 chunk 201 optimal weight: 0.2980 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 241 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 208 ASN B 30 ASN B 96 ASN B 145 ASN B 157 ASN B 529 GLN B 567 GLN ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN B 989 GLN B1172 ASN C 168 ASN C 208 ASN D 30 ASN D 96 ASN D 145 ASN D 157 ASN D 529 GLN D 567 GLN D 676 GLN ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 ASN ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 928 ASN D 989 GLN D1172 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23488 Z= 0.163 Angle : 0.607 11.946 31818 Z= 0.320 Chirality : 0.042 0.250 3436 Planarity : 0.004 0.050 3876 Dihedral : 11.641 171.900 3621 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.83 % Allowed : 15.71 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.16), residues: 2612 helix: -0.88 (0.15), residues: 1148 sheet: -2.20 (0.34), residues: 238 loop : -2.83 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 890 HIS 0.003 0.001 HIS B 759 PHE 0.014 0.001 PHE B1149 TYR 0.018 0.001 TYR B 294 ARG 0.005 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 423 time to evaluate : 2.827 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 145 ASN cc_start: 0.8855 (m-40) cc_final: 0.8545 (t0) REVERT: A 148 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8153 (ttmm) REVERT: A 174 GLU cc_start: 0.8225 (tt0) cc_final: 0.7965 (tt0) REVERT: A 176 GLU cc_start: 0.7940 (pm20) cc_final: 0.7387 (pm20) REVERT: A 219 GLU cc_start: 0.8258 (pt0) cc_final: 0.7358 (pm20) REVERT: A 228 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 231 ASN cc_start: 0.8297 (t0) cc_final: 0.7873 (t0) REVERT: B 5 GLU cc_start: 0.8316 (tt0) cc_final: 0.8088 (tt0) REVERT: B 174 ARG cc_start: 0.8394 (tpp80) cc_final: 0.8158 (ttm-80) REVERT: B 179 ASN cc_start: 0.7543 (m110) cc_final: 0.7250 (m110) REVERT: B 315 PHE cc_start: 0.8320 (t80) cc_final: 0.8040 (t80) REVERT: B 321 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8483 (tt) REVERT: B 330 GLU cc_start: 0.7361 (mp0) cc_final: 0.7120 (pp20) REVERT: B 456 MET cc_start: 0.7854 (mtt) cc_final: 0.7649 (mtp) REVERT: B 522 LYS cc_start: 0.8812 (tttt) cc_final: 0.8246 (tttp) REVERT: B 524 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: B 527 ASN cc_start: 0.8460 (t0) cc_final: 0.7922 (t0) REVERT: B 754 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8226 (mp0) REVERT: B 858 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 941 GLN cc_start: 0.8320 (tp40) cc_final: 0.7883 (tp40) REVERT: B 1027 PHE cc_start: 0.8580 (t80) cc_final: 0.8134 (t80) REVERT: B 1033 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7811 (ttm-80) REVERT: B 1132 SER cc_start: 0.8708 (t) cc_final: 0.8183 (m) REVERT: B 1137 MET cc_start: 0.8829 (mtp) cc_final: 0.8584 (mtp) REVERT: C 148 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8119 (ttmm) REVERT: C 174 GLU cc_start: 0.8230 (tt0) cc_final: 0.7975 (tt0) REVERT: C 176 GLU cc_start: 0.7988 (pm20) cc_final: 0.7457 (pm20) REVERT: C 219 GLU cc_start: 0.7979 (pt0) cc_final: 0.7383 (pm20) REVERT: C 221 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 228 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7893 (tm-30) REVERT: C 231 ASN cc_start: 0.8277 (t0) cc_final: 0.7844 (t0) REVERT: D 5 GLU cc_start: 0.8306 (tt0) cc_final: 0.8042 (tt0) REVERT: D 87 THR cc_start: 0.4682 (OUTLIER) cc_final: 0.4470 (m) REVERT: D 88 GLU cc_start: 0.4338 (OUTLIER) cc_final: 0.4121 (pp20) REVERT: D 174 ARG cc_start: 0.8428 (tpp80) cc_final: 0.8193 (ttm-80) REVERT: D 179 ASN cc_start: 0.7531 (m110) cc_final: 0.7239 (m110) REVERT: D 315 PHE cc_start: 0.8320 (t80) cc_final: 0.8043 (t80) REVERT: D 321 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8496 (tt) REVERT: D 330 GLU cc_start: 0.7354 (mp0) cc_final: 0.7125 (pp20) REVERT: D 522 LYS cc_start: 0.8820 (tttt) cc_final: 0.8222 (tttp) REVERT: D 524 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: D 527 ASN cc_start: 0.8444 (t0) cc_final: 0.7918 (t0) REVERT: D 754 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8228 (mp0) REVERT: D 786 ASP cc_start: 0.8910 (m-30) cc_final: 0.8679 (m-30) REVERT: D 858 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7703 (mt-10) REVERT: D 954 LEU cc_start: 0.8287 (tp) cc_final: 0.8086 (tp) REVERT: D 1027 PHE cc_start: 0.8581 (t80) cc_final: 0.8132 (t80) REVERT: D 1033 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.7816 (ttm-80) REVERT: D 1132 SER cc_start: 0.8709 (t) cc_final: 0.8084 (p) REVERT: D 1137 MET cc_start: 0.8841 (mtp) cc_final: 0.8584 (mtp) outliers start: 44 outliers final: 17 residues processed: 453 average time/residue: 0.3642 time to fit residues: 251.6292 Evaluate side-chains 353 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 330 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 524 TYR Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 1172 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 201 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 241 optimal weight: 7.9990 chunk 261 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 238 ASN B 676 GLN ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN C 157 ASN D 238 ASN ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 906 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23488 Z= 0.311 Angle : 0.649 12.541 31818 Z= 0.339 Chirality : 0.044 0.257 3436 Planarity : 0.004 0.041 3876 Dihedral : 11.578 167.743 3621 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.62 % Allowed : 18.25 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.16), residues: 2612 helix: -0.53 (0.15), residues: 1138 sheet: -2.05 (0.34), residues: 238 loop : -2.67 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1086 HIS 0.003 0.001 HIS D 714 PHE 0.015 0.002 PHE B 530 TYR 0.020 0.002 TYR B 258 ARG 0.004 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 352 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8182 (ttmm) REVERT: A 176 GLU cc_start: 0.7881 (pm20) cc_final: 0.7367 (pm20) REVERT: A 219 GLU cc_start: 0.7928 (pt0) cc_final: 0.7486 (pm20) REVERT: A 231 ASN cc_start: 0.8318 (t0) cc_final: 0.8082 (t0) REVERT: B 5 GLU cc_start: 0.8338 (tt0) cc_final: 0.8105 (tt0) REVERT: B 174 ARG cc_start: 0.8360 (tpp80) cc_final: 0.8149 (ttm-80) REVERT: B 179 ASN cc_start: 0.7708 (m-40) cc_final: 0.7437 (m110) REVERT: B 321 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8488 (tt) REVERT: B 354 GLU cc_start: 0.8451 (tp30) cc_final: 0.8237 (tp30) REVERT: B 514 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8342 (ptpt) REVERT: B 522 LYS cc_start: 0.8824 (tttt) cc_final: 0.8330 (tttt) REVERT: B 524 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: B 525 PHE cc_start: 0.8670 (m-10) cc_final: 0.8392 (m-10) REVERT: B 527 ASN cc_start: 0.8501 (t0) cc_final: 0.8085 (t0) REVERT: B 531 MET cc_start: 0.8275 (mtp) cc_final: 0.7917 (mtm) REVERT: B 543 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7385 (mtm-85) REVERT: B 557 ILE cc_start: 0.9063 (mt) cc_final: 0.8827 (mm) REVERT: B 589 PRO cc_start: 0.5578 (Cg_exo) cc_final: 0.5150 (Cg_endo) REVERT: B 674 GLU cc_start: 0.8778 (tp30) cc_final: 0.8474 (tp30) REVERT: B 754 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8043 (mp0) REVERT: B 939 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: B 1033 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.7840 (ttm-80) REVERT: B 1132 SER cc_start: 0.8711 (t) cc_final: 0.8129 (p) REVERT: B 1137 MET cc_start: 0.8899 (mtp) cc_final: 0.8629 (mtp) REVERT: B 1185 TYR cc_start: 0.9165 (t80) cc_final: 0.8662 (t80) REVERT: C 148 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8179 (ttmm) REVERT: C 176 GLU cc_start: 0.7921 (pm20) cc_final: 0.7420 (pm20) REVERT: C 219 GLU cc_start: 0.7969 (pt0) cc_final: 0.7465 (pm20) REVERT: C 228 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8111 (tm-30) REVERT: C 231 ASN cc_start: 0.8315 (t0) cc_final: 0.8074 (t0) REVERT: D 5 GLU cc_start: 0.8356 (tt0) cc_final: 0.8106 (tt0) REVERT: D 174 ARG cc_start: 0.8367 (tpp80) cc_final: 0.8156 (ttm-80) REVERT: D 179 ASN cc_start: 0.7696 (m-40) cc_final: 0.7428 (m110) REVERT: D 321 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8488 (tt) REVERT: D 354 GLU cc_start: 0.8446 (tp30) cc_final: 0.8232 (tp30) REVERT: D 514 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8320 (ptpt) REVERT: D 522 LYS cc_start: 0.8803 (tttt) cc_final: 0.8360 (tttt) REVERT: D 524 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: D 525 PHE cc_start: 0.8685 (m-10) cc_final: 0.8398 (m-10) REVERT: D 527 ASN cc_start: 0.8478 (t0) cc_final: 0.8075 (t0) REVERT: D 531 MET cc_start: 0.8277 (mtp) cc_final: 0.7919 (mtm) REVERT: D 543 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: D 557 ILE cc_start: 0.9052 (mt) cc_final: 0.8819 (mm) REVERT: D 589 PRO cc_start: 0.5581 (Cg_exo) cc_final: 0.5159 (Cg_endo) REVERT: D 674 GLU cc_start: 0.8781 (tp30) cc_final: 0.8475 (tp30) REVERT: D 754 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8187 (mp0) REVERT: D 786 ASP cc_start: 0.9061 (m-30) cc_final: 0.8657 (m-30) REVERT: D 939 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: D 1033 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7842 (ttm-80) REVERT: D 1132 SER cc_start: 0.8714 (t) cc_final: 0.8131 (p) REVERT: D 1137 MET cc_start: 0.8914 (mtp) cc_final: 0.8643 (mtp) REVERT: D 1185 TYR cc_start: 0.9170 (t80) cc_final: 0.8676 (t80) outliers start: 63 outliers final: 38 residues processed: 386 average time/residue: 0.3708 time to fit residues: 219.2987 Evaluate side-chains 361 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 316 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 524 TYR Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 257 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 732 ASN ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23488 Z= 0.237 Angle : 0.599 10.262 31818 Z= 0.313 Chirality : 0.043 0.260 3436 Planarity : 0.003 0.038 3876 Dihedral : 11.495 169.866 3618 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.53 % Allowed : 20.62 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2612 helix: -0.16 (0.16), residues: 1126 sheet: -2.01 (0.34), residues: 246 loop : -2.44 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 602 HIS 0.003 0.001 HIS C 190 PHE 0.012 0.001 PHE D 521 TYR 0.020 0.001 TYR D 258 ARG 0.006 0.000 ARG D1054 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 355 time to evaluate : 2.522 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 148 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8183 (ttmm) REVERT: A 216 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7586 (t) REVERT: A 219 GLU cc_start: 0.7933 (pt0) cc_final: 0.7403 (pm20) REVERT: A 231 ASN cc_start: 0.8236 (t0) cc_final: 0.7887 (t0) REVERT: B 5 GLU cc_start: 0.8372 (tt0) cc_final: 0.8092 (tt0) REVERT: B 82 ARG cc_start: 0.7197 (mtm180) cc_final: 0.6497 (mtm180) REVERT: B 174 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7943 (ttm-80) REVERT: B 179 ASN cc_start: 0.7716 (m-40) cc_final: 0.7438 (m110) REVERT: B 321 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8475 (tt) REVERT: B 354 GLU cc_start: 0.8515 (tp30) cc_final: 0.8270 (tp30) REVERT: B 514 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8322 (ptpt) REVERT: B 522 LYS cc_start: 0.8863 (tttt) cc_final: 0.8353 (tttt) REVERT: B 524 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.6793 (m-80) REVERT: B 527 ASN cc_start: 0.8519 (t0) cc_final: 0.8016 (t0) REVERT: B 531 MET cc_start: 0.8272 (mtp) cc_final: 0.7848 (mtm) REVERT: B 543 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7223 (mtm-85) REVERT: B 557 ILE cc_start: 0.9045 (mt) cc_final: 0.8681 (mm) REVERT: B 589 PRO cc_start: 0.5636 (Cg_exo) cc_final: 0.5183 (Cg_endo) REVERT: B 674 GLU cc_start: 0.8781 (tp30) cc_final: 0.8383 (tp30) REVERT: B 696 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 722 MET cc_start: 0.7749 (ttm) cc_final: 0.7517 (ttm) REVERT: B 746 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.6139 (tpp) REVERT: B 754 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8059 (mp0) REVERT: B 841 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7661 (tp) REVERT: B 858 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7699 (mt-10) REVERT: B 939 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: B 1033 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.7822 (ttm-80) REVERT: B 1132 SER cc_start: 0.8711 (t) cc_final: 0.8231 (m) REVERT: B 1137 MET cc_start: 0.8890 (mtp) cc_final: 0.8632 (mtp) REVERT: B 1185 TYR cc_start: 0.9107 (t80) cc_final: 0.8624 (t80) REVERT: C 148 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8176 (ttmm) REVERT: C 228 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 231 ASN cc_start: 0.8219 (t0) cc_final: 0.7861 (t0) REVERT: D 5 GLU cc_start: 0.8369 (tt0) cc_final: 0.8098 (tt0) REVERT: D 174 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7951 (ttm-80) REVERT: D 179 ASN cc_start: 0.7717 (m-40) cc_final: 0.7437 (m110) REVERT: D 321 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8475 (tt) REVERT: D 354 GLU cc_start: 0.8511 (tp30) cc_final: 0.8264 (tp30) REVERT: D 514 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8300 (ptpt) REVERT: D 522 LYS cc_start: 0.8806 (tttt) cc_final: 0.8311 (tttt) REVERT: D 524 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.6750 (m-80) REVERT: D 527 ASN cc_start: 0.8541 (t0) cc_final: 0.8019 (t0) REVERT: D 531 MET cc_start: 0.8273 (mtp) cc_final: 0.7850 (mtm) REVERT: D 543 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7224 (mtm-85) REVERT: D 557 ILE cc_start: 0.9041 (mt) cc_final: 0.8679 (mm) REVERT: D 589 PRO cc_start: 0.5637 (Cg_exo) cc_final: 0.5195 (Cg_endo) REVERT: D 674 GLU cc_start: 0.8780 (tp30) cc_final: 0.8382 (tp30) REVERT: D 696 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7813 (mt-10) REVERT: D 722 MET cc_start: 0.7802 (ttm) cc_final: 0.7570 (ttm) REVERT: D 746 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.6138 (tpp) REVERT: D 754 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8191 (mp0) REVERT: D 786 ASP cc_start: 0.8975 (m-30) cc_final: 0.8606 (m-30) REVERT: D 841 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7669 (tp) REVERT: D 858 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7695 (mt-10) REVERT: D 939 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: D 1033 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.7821 (ttm-80) REVERT: D 1132 SER cc_start: 0.8710 (t) cc_final: 0.8230 (m) REVERT: D 1137 MET cc_start: 0.8905 (mtp) cc_final: 0.8641 (mtp) REVERT: D 1185 TYR cc_start: 0.9103 (t80) cc_final: 0.8634 (t80) outliers start: 85 outliers final: 52 residues processed: 403 average time/residue: 0.3753 time to fit residues: 231.4594 Evaluate side-chains 391 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 328 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 746 MET Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1090 CYS Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1174 ILE Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 355 TRP Chi-restraints excluded: chain D residue 524 TYR Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1174 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 177 optimal weight: 0.0670 chunk 0 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 731 ASN B 797 HIS ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 ASN D 797 HIS ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23488 Z= 0.148 Angle : 0.567 9.434 31818 Z= 0.294 Chirality : 0.041 0.235 3436 Planarity : 0.003 0.049 3876 Dihedral : 11.433 172.734 3618 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.53 % Allowed : 20.24 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.68 (0.17), residues: 2612 helix: 0.17 (0.16), residues: 1136 sheet: -1.88 (0.35), residues: 240 loop : -2.23 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.003 0.001 HIS C 233 PHE 0.010 0.001 PHE D1149 TYR 0.025 0.001 TYR D 258 ARG 0.006 0.000 ARG D1054 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 361 time to evaluate : 2.469 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 148 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8161 (ttmm) REVERT: A 174 GLU cc_start: 0.8415 (tt0) cc_final: 0.8140 (tt0) REVERT: A 176 GLU cc_start: 0.8087 (pm20) cc_final: 0.7666 (pm20) REVERT: A 231 ASN cc_start: 0.8345 (t0) cc_final: 0.7915 (t0) REVERT: B 5 GLU cc_start: 0.8353 (tt0) cc_final: 0.8050 (tt0) REVERT: B 179 ASN cc_start: 0.7676 (m-40) cc_final: 0.7395 (m110) REVERT: B 321 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8388 (tt) REVERT: B 354 GLU cc_start: 0.8504 (tp30) cc_final: 0.8269 (tp30) REVERT: B 514 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8281 (ptpt) REVERT: B 522 LYS cc_start: 0.8906 (tttt) cc_final: 0.8074 (tttp) REVERT: B 524 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: B 527 ASN cc_start: 0.8471 (t0) cc_final: 0.7953 (t0) REVERT: B 531 MET cc_start: 0.8234 (mtp) cc_final: 0.7873 (mtm) REVERT: B 557 ILE cc_start: 0.9009 (mt) cc_final: 0.8725 (mm) REVERT: B 589 PRO cc_start: 0.5437 (Cg_exo) cc_final: 0.4893 (Cg_endo) REVERT: B 674 GLU cc_start: 0.8739 (tp30) cc_final: 0.8355 (tp30) REVERT: B 696 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 754 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8026 (mp0) REVERT: B 841 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7697 (tp) REVERT: B 858 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 939 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: B 958 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8693 (t) REVERT: B 1033 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7727 (ttm-80) REVERT: B 1073 ARG cc_start: 0.7628 (ttt180) cc_final: 0.7255 (mtp-110) REVERT: B 1131 MET cc_start: 0.8622 (tpp) cc_final: 0.8316 (mmm) REVERT: B 1132 SER cc_start: 0.8754 (t) cc_final: 0.8307 (m) REVERT: B 1137 MET cc_start: 0.8768 (mtp) cc_final: 0.8560 (mtp) REVERT: B 1185 TYR cc_start: 0.8982 (t80) cc_final: 0.8653 (t80) REVERT: C 148 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8147 (ttmm) REVERT: C 174 GLU cc_start: 0.8409 (tt0) cc_final: 0.8130 (tt0) REVERT: C 176 GLU cc_start: 0.8097 (pm20) cc_final: 0.7669 (pm20) REVERT: C 228 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8242 (tm-30) REVERT: C 231 ASN cc_start: 0.8342 (t0) cc_final: 0.7901 (t0) REVERT: D 5 GLU cc_start: 0.8346 (tt0) cc_final: 0.8055 (tt0) REVERT: D 38 VAL cc_start: 0.8146 (m) cc_final: 0.7673 (p) REVERT: D 179 ASN cc_start: 0.7675 (m-40) cc_final: 0.7391 (m110) REVERT: D 321 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8454 (tt) REVERT: D 354 GLU cc_start: 0.8506 (tp30) cc_final: 0.8270 (tp30) REVERT: D 499 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7929 (mtmm) REVERT: D 514 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8269 (ptpt) REVERT: D 522 LYS cc_start: 0.8881 (tttt) cc_final: 0.8042 (tttp) REVERT: D 524 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: D 527 ASN cc_start: 0.8453 (t0) cc_final: 0.7988 (t0) REVERT: D 531 MET cc_start: 0.8211 (mtp) cc_final: 0.7827 (mtm) REVERT: D 543 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7124 (mtm-85) REVERT: D 557 ILE cc_start: 0.9007 (mt) cc_final: 0.8720 (mm) REVERT: D 589 PRO cc_start: 0.5444 (Cg_exo) cc_final: 0.4895 (Cg_endo) REVERT: D 674 GLU cc_start: 0.8743 (tp30) cc_final: 0.8359 (tp30) REVERT: D 696 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7813 (mt-10) REVERT: D 754 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8031 (mp0) REVERT: D 841 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7694 (tp) REVERT: D 858 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7615 (mt-10) REVERT: D 939 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: D 958 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8674 (t) REVERT: D 1033 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7682 (ttm-80) REVERT: D 1073 ARG cc_start: 0.7638 (ttt180) cc_final: 0.7259 (mtp-110) REVERT: D 1131 MET cc_start: 0.8599 (tpp) cc_final: 0.8258 (mmm) REVERT: D 1132 SER cc_start: 0.8754 (t) cc_final: 0.8306 (m) REVERT: D 1137 MET cc_start: 0.8782 (mtp) cc_final: 0.8569 (mtp) REVERT: D 1185 TYR cc_start: 0.8978 (t80) cc_final: 0.8665 (t80) outliers start: 85 outliers final: 47 residues processed: 407 average time/residue: 0.3994 time to fit residues: 247.9677 Evaluate side-chains 374 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 316 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1090 CYS Chi-restraints excluded: chain B residue 1174 ILE Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain D residue 524 TYR Chi-restraints excluded: chain D residue 545 THR Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1174 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 chunk 213 optimal weight: 0.3980 chunk 119 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 731 ASN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 ASN ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23488 Z= 0.145 Angle : 0.560 7.835 31818 Z= 0.291 Chirality : 0.041 0.229 3436 Planarity : 0.003 0.045 3876 Dihedral : 11.478 172.397 3618 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.74 % Allowed : 20.37 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.46 (0.17), residues: 2612 helix: 0.39 (0.16), residues: 1138 sheet: -1.96 (0.33), residues: 250 loop : -2.10 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 602 HIS 0.003 0.001 HIS D 797 PHE 0.011 0.001 PHE D 521 TYR 0.028 0.001 TYR B 115 ARG 0.007 0.000 ARG D1054 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 341 time to evaluate : 2.579 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 148 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8173 (ttmm) REVERT: A 176 GLU cc_start: 0.8096 (pm20) cc_final: 0.7609 (pm20) REVERT: A 231 ASN cc_start: 0.8343 (t0) cc_final: 0.7911 (t0) REVERT: B 5 GLU cc_start: 0.8334 (tt0) cc_final: 0.8127 (tt0) REVERT: B 179 ASN cc_start: 0.7786 (m-40) cc_final: 0.7466 (m110) REVERT: B 321 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8375 (tt) REVERT: B 354 GLU cc_start: 0.8523 (tp30) cc_final: 0.8266 (tp30) REVERT: B 514 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8254 (ptpt) REVERT: B 522 LYS cc_start: 0.8941 (tttt) cc_final: 0.8412 (tttt) REVERT: B 524 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: B 527 ASN cc_start: 0.8571 (t0) cc_final: 0.8121 (t0) REVERT: B 531 MET cc_start: 0.8210 (mtp) cc_final: 0.7892 (mtm) REVERT: B 589 PRO cc_start: 0.5481 (Cg_exo) cc_final: 0.4910 (Cg_endo) REVERT: B 674 GLU cc_start: 0.8759 (tp30) cc_final: 0.8378 (tp30) REVERT: B 696 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7827 (mt-10) REVERT: B 754 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8018 (mp0) REVERT: B 841 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7749 (tp) REVERT: B 858 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7621 (mt-10) REVERT: B 935 ARG cc_start: 0.7810 (ptp90) cc_final: 0.7572 (ptp90) REVERT: B 939 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: B 1033 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7745 (ttm-80) REVERT: B 1073 ARG cc_start: 0.7577 (ttt180) cc_final: 0.7240 (mtp-110) REVERT: B 1131 MET cc_start: 0.8613 (tpp) cc_final: 0.8384 (mmm) REVERT: B 1132 SER cc_start: 0.8793 (t) cc_final: 0.8409 (m) REVERT: B 1137 MET cc_start: 0.8753 (mtp) cc_final: 0.8517 (mtp) REVERT: B 1185 TYR cc_start: 0.8929 (t80) cc_final: 0.8671 (t80) REVERT: C 148 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8160 (ttmm) REVERT: C 176 GLU cc_start: 0.8095 (pm20) cc_final: 0.7616 (pm20) REVERT: C 228 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8188 (tm-30) REVERT: C 231 ASN cc_start: 0.8336 (t0) cc_final: 0.7900 (t0) REVERT: D 5 GLU cc_start: 0.8330 (tt0) cc_final: 0.8030 (tt0) REVERT: D 38 VAL cc_start: 0.8165 (m) cc_final: 0.7735 (p) REVERT: D 179 ASN cc_start: 0.7786 (m-40) cc_final: 0.7463 (m110) REVERT: D 321 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8377 (tt) REVERT: D 354 GLU cc_start: 0.8493 (tp30) cc_final: 0.8236 (tp30) REVERT: D 514 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8265 (ptpt) REVERT: D 522 LYS cc_start: 0.8898 (tttt) cc_final: 0.8331 (tttt) REVERT: D 524 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: D 527 ASN cc_start: 0.8565 (t0) cc_final: 0.8115 (t0) REVERT: D 530 PHE cc_start: 0.8288 (t80) cc_final: 0.8025 (t80) REVERT: D 531 MET cc_start: 0.8202 (mtp) cc_final: 0.7943 (mtm) REVERT: D 557 ILE cc_start: 0.9021 (mt) cc_final: 0.8685 (mm) REVERT: D 589 PRO cc_start: 0.5479 (Cg_exo) cc_final: 0.4918 (Cg_endo) REVERT: D 674 GLU cc_start: 0.8764 (tp30) cc_final: 0.8380 (tp30) REVERT: D 696 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7827 (mt-10) REVERT: D 754 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8037 (mp0) REVERT: D 841 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7734 (tp) REVERT: D 858 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7617 (mt-10) REVERT: D 935 ARG cc_start: 0.7812 (ptp90) cc_final: 0.7573 (ptp90) REVERT: D 939 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6812 (pm20) REVERT: D 958 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8716 (t) REVERT: D 1033 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7724 (ttm-80) REVERT: D 1073 ARG cc_start: 0.7580 (ttt180) cc_final: 0.7241 (mtp-110) REVERT: D 1131 MET cc_start: 0.8614 (tpp) cc_final: 0.8383 (mmm) REVERT: D 1132 SER cc_start: 0.8775 (t) cc_final: 0.8378 (m) REVERT: D 1137 MET cc_start: 0.8758 (mtp) cc_final: 0.8532 (mtp) REVERT: D 1185 TYR cc_start: 0.8927 (t80) cc_final: 0.8665 (t80) outliers start: 90 outliers final: 59 residues processed: 388 average time/residue: 0.3663 time to fit residues: 221.1070 Evaluate side-chains 381 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 313 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1090 CYS Chi-restraints excluded: chain B residue 1174 ILE Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 355 TRP Chi-restraints excluded: chain D residue 524 TYR Chi-restraints excluded: chain D residue 545 THR Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 TRP Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 1004 ILE Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1174 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 216 optimal weight: 0.0070 chunk 143 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 overall best weight: 2.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 GLN ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN D 853 GLN D 989 GLN ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23488 Z= 0.328 Angle : 0.650 8.846 31818 Z= 0.337 Chirality : 0.045 0.253 3436 Planarity : 0.004 0.045 3876 Dihedral : 11.620 165.799 3618 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.07 % Allowed : 21.07 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.66 (0.17), residues: 2612 helix: 0.20 (0.16), residues: 1144 sheet: -2.07 (0.33), residues: 256 loop : -2.20 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 178 HIS 0.006 0.001 HIS D 797 PHE 0.015 0.002 PHE B 225 TYR 0.026 0.002 TYR B 262 ARG 0.007 0.001 ARG B1054 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 335 time to evaluate : 2.519 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 148 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8238 (ttmm) REVERT: A 174 GLU cc_start: 0.8446 (tt0) cc_final: 0.8132 (tt0) REVERT: A 231 ASN cc_start: 0.8369 (t0) cc_final: 0.8076 (t0) REVERT: B 5 GLU cc_start: 0.8392 (tt0) cc_final: 0.8185 (tt0) REVERT: B 179 ASN cc_start: 0.7873 (m-40) cc_final: 0.7534 (m110) REVERT: B 321 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8424 (tt) REVERT: B 527 ASN cc_start: 0.8505 (t0) cc_final: 0.7917 (t0) REVERT: B 531 MET cc_start: 0.8348 (mtp) cc_final: 0.8018 (mtm) REVERT: B 589 PRO cc_start: 0.5755 (Cg_exo) cc_final: 0.5302 (Cg_endo) REVERT: B 674 GLU cc_start: 0.8759 (tp30) cc_final: 0.8357 (tp30) REVERT: B 696 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7790 (mt-10) REVERT: B 815 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7794 (mt-10) REVERT: B 841 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7684 (tp) REVERT: B 939 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7016 (pm20) REVERT: B 958 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8677 (t) REVERT: B 1033 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7782 (ttm-80) REVERT: B 1035 MET cc_start: 0.6031 (ppp) cc_final: 0.5741 (ppp) REVERT: B 1073 ARG cc_start: 0.7667 (ttt180) cc_final: 0.7257 (mtp-110) REVERT: B 1131 MET cc_start: 0.8538 (tpp) cc_final: 0.8283 (mmm) REVERT: B 1132 SER cc_start: 0.8775 (t) cc_final: 0.8378 (m) REVERT: B 1137 MET cc_start: 0.8921 (mtp) cc_final: 0.8657 (mtp) REVERT: B 1185 TYR cc_start: 0.9119 (t80) cc_final: 0.8651 (t80) REVERT: C 148 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8241 (ttmm) REVERT: C 174 GLU cc_start: 0.8457 (tt0) cc_final: 0.8142 (tt0) REVERT: C 228 GLU cc_start: 0.8657 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 231 ASN cc_start: 0.8321 (t0) cc_final: 0.8024 (t0) REVERT: D 179 ASN cc_start: 0.7872 (m-40) cc_final: 0.7534 (m110) REVERT: D 321 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8440 (tt) REVERT: D 522 LYS cc_start: 0.8832 (tttt) cc_final: 0.8583 (tttt) REVERT: D 527 ASN cc_start: 0.8569 (t0) cc_final: 0.8042 (t0) REVERT: D 531 MET cc_start: 0.8348 (mtp) cc_final: 0.7933 (mtm) REVERT: D 557 ILE cc_start: 0.9001 (mt) cc_final: 0.8662 (mm) REVERT: D 589 PRO cc_start: 0.5759 (Cg_exo) cc_final: 0.5314 (Cg_endo) REVERT: D 674 GLU cc_start: 0.8763 (tp30) cc_final: 0.8362 (tp30) REVERT: D 696 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7799 (mt-10) REVERT: D 722 MET cc_start: 0.7759 (ttm) cc_final: 0.7545 (ttm) REVERT: D 841 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7668 (tp) REVERT: D 939 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: D 958 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8679 (t) REVERT: D 978 ASN cc_start: 0.8702 (m-40) cc_final: 0.8130 (m-40) REVERT: D 986 MET cc_start: 0.7899 (mtm) cc_final: 0.7646 (mtp) REVERT: D 995 TYR cc_start: 0.8902 (m-80) cc_final: 0.8522 (m-10) REVERT: D 1035 MET cc_start: 0.6020 (ppp) cc_final: 0.5754 (ppp) REVERT: D 1073 ARG cc_start: 0.7671 (ttt180) cc_final: 0.7258 (mtp-110) REVERT: D 1115 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7591 (mm) REVERT: D 1131 MET cc_start: 0.8536 (tpp) cc_final: 0.8279 (mmm) REVERT: D 1132 SER cc_start: 0.8784 (t) cc_final: 0.8389 (m) REVERT: D 1137 MET cc_start: 0.8923 (mtp) cc_final: 0.8598 (mtp) REVERT: D 1185 TYR cc_start: 0.9123 (t80) cc_final: 0.8701 (t80) outliers start: 98 outliers final: 69 residues processed: 389 average time/residue: 0.3905 time to fit residues: 235.5488 Evaluate side-chains 394 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 316 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1090 CYS Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 355 TRP Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 TRP Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 977 THR Chi-restraints excluded: chain D residue 1004 ILE Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23488 Z= 0.221 Angle : 0.614 9.256 31818 Z= 0.317 Chirality : 0.043 0.251 3436 Planarity : 0.004 0.048 3876 Dihedral : 11.647 169.093 3618 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.24 % Allowed : 22.19 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.58 (0.17), residues: 2612 helix: 0.28 (0.16), residues: 1130 sheet: -2.34 (0.30), residues: 284 loop : -2.03 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 362 HIS 0.005 0.001 HIS D 797 PHE 0.014 0.001 PHE D 328 TYR 0.029 0.001 TYR B 258 ARG 0.008 0.001 ARG D1054 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 333 time to evaluate : 2.432 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 148 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8199 (ttmm) REVERT: A 174 GLU cc_start: 0.8377 (tt0) cc_final: 0.8033 (tp30) REVERT: A 231 ASN cc_start: 0.8373 (t0) cc_final: 0.7935 (t0) REVERT: B 5 GLU cc_start: 0.8383 (tt0) cc_final: 0.8167 (tt0) REVERT: B 179 ASN cc_start: 0.7868 (m-40) cc_final: 0.7526 (m110) REVERT: B 321 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8427 (tt) REVERT: B 362 TRP cc_start: 0.7648 (t60) cc_final: 0.7320 (t60) REVERT: B 456 MET cc_start: 0.7917 (mmm) cc_final: 0.7359 (mmt) REVERT: B 527 ASN cc_start: 0.8681 (t0) cc_final: 0.7856 (t0) REVERT: B 531 MET cc_start: 0.8336 (mtp) cc_final: 0.8080 (mtm) REVERT: B 543 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7355 (mtm-85) REVERT: B 841 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7619 (tp) REVERT: B 858 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 939 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: B 958 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8672 (t) REVERT: B 1027 PHE cc_start: 0.8678 (t80) cc_final: 0.8397 (t80) REVERT: B 1033 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7621 (ttm-80) REVERT: B 1035 MET cc_start: 0.5978 (ppp) cc_final: 0.5664 (ppp) REVERT: B 1064 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7852 (ttmm) REVERT: B 1073 ARG cc_start: 0.7660 (ttt180) cc_final: 0.7273 (mtp-110) REVERT: B 1132 SER cc_start: 0.8768 (t) cc_final: 0.8389 (m) REVERT: B 1137 MET cc_start: 0.8833 (mtp) cc_final: 0.8535 (mtp) REVERT: B 1185 TYR cc_start: 0.9046 (t80) cc_final: 0.8646 (t80) REVERT: C 148 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8231 (ttmm) REVERT: C 174 GLU cc_start: 0.8427 (tt0) cc_final: 0.8078 (tp30) REVERT: C 228 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 231 ASN cc_start: 0.8347 (t0) cc_final: 0.7927 (t0) REVERT: D 5 GLU cc_start: 0.8350 (tt0) cc_final: 0.8041 (pt0) REVERT: D 179 ASN cc_start: 0.7871 (m-40) cc_final: 0.7529 (m110) REVERT: D 321 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8427 (tt) REVERT: D 362 TRP cc_start: 0.7644 (t60) cc_final: 0.7315 (t60) REVERT: D 456 MET cc_start: 0.7863 (mmm) cc_final: 0.7422 (mmm) REVERT: D 527 ASN cc_start: 0.8567 (t0) cc_final: 0.8078 (t0) REVERT: D 531 MET cc_start: 0.8376 (mtp) cc_final: 0.7959 (mtm) REVERT: D 543 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7139 (mtm-85) REVERT: D 557 ILE cc_start: 0.8995 (mt) cc_final: 0.8645 (mm) REVERT: D 696 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7750 (mt-10) REVERT: D 722 MET cc_start: 0.7746 (ttm) cc_final: 0.7502 (ttm) REVERT: D 841 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7623 (tp) REVERT: D 858 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 939 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: D 958 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8684 (t) REVERT: D 1027 PHE cc_start: 0.8673 (t80) cc_final: 0.8387 (t80) REVERT: D 1035 MET cc_start: 0.5986 (ppp) cc_final: 0.5723 (ppp) REVERT: D 1064 LYS cc_start: 0.8291 (mmtm) cc_final: 0.8081 (ttmm) REVERT: D 1073 ARG cc_start: 0.7661 (ttt180) cc_final: 0.7273 (mtp-110) REVERT: D 1115 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7486 (mm) REVERT: D 1132 SER cc_start: 0.8774 (t) cc_final: 0.8385 (m) REVERT: D 1137 MET cc_start: 0.8839 (mtp) cc_final: 0.8537 (mtp) REVERT: D 1185 TYR cc_start: 0.9044 (t80) cc_final: 0.8694 (t80) outliers start: 78 outliers final: 67 residues processed: 375 average time/residue: 0.3466 time to fit residues: 200.2816 Evaluate side-chains 391 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 315 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1090 CYS Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 355 TRP Chi-restraints excluded: chain D residue 487 TYR Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 TRP Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 1004 ILE Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.9980 chunk 245 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 chunk 156 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23488 Z= 0.202 Angle : 0.609 9.631 31818 Z= 0.313 Chirality : 0.043 0.243 3436 Planarity : 0.004 0.047 3876 Dihedral : 11.643 169.591 3618 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.57 % Allowed : 22.11 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.45 (0.17), residues: 2612 helix: 0.32 (0.16), residues: 1132 sheet: -1.98 (0.33), residues: 246 loop : -2.00 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 362 HIS 0.007 0.001 HIS B 759 PHE 0.016 0.001 PHE B 328 TYR 0.039 0.001 TYR D 258 ARG 0.009 0.001 ARG B1054 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 334 time to evaluate : 2.619 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 148 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8187 (ttmm) REVERT: A 174 GLU cc_start: 0.8380 (tt0) cc_final: 0.8019 (tp30) REVERT: A 231 ASN cc_start: 0.8352 (t0) cc_final: 0.7970 (t0) REVERT: B 5 GLU cc_start: 0.8383 (tt0) cc_final: 0.8156 (tt0) REVERT: B 167 LYS cc_start: 0.8931 (tppt) cc_final: 0.8386 (mmmt) REVERT: B 179 ASN cc_start: 0.7892 (m-40) cc_final: 0.7540 (m110) REVERT: B 321 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8392 (tt) REVERT: B 362 TRP cc_start: 0.7630 (t60) cc_final: 0.7233 (t60) REVERT: B 527 ASN cc_start: 0.8662 (t0) cc_final: 0.7829 (t0) REVERT: B 531 MET cc_start: 0.8451 (mtp) cc_final: 0.8169 (mtm) REVERT: B 543 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.7200 (mtm-85) REVERT: B 841 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7649 (tp) REVERT: B 858 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7695 (mt-10) REVERT: B 939 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: B 958 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8713 (t) REVERT: B 1033 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7590 (ttm-80) REVERT: B 1035 MET cc_start: 0.5975 (ppp) cc_final: 0.5660 (ppp) REVERT: B 1064 LYS cc_start: 0.8049 (mmtm) cc_final: 0.7837 (ttmm) REVERT: B 1073 ARG cc_start: 0.7650 (ttt180) cc_final: 0.7278 (mtp-110) REVERT: B 1115 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7509 (mm) REVERT: B 1132 SER cc_start: 0.8815 (t) cc_final: 0.8427 (m) REVERT: B 1137 MET cc_start: 0.8792 (mtp) cc_final: 0.8513 (mtp) REVERT: B 1185 TYR cc_start: 0.9010 (t80) cc_final: 0.8615 (t80) REVERT: C 148 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8192 (ttmm) REVERT: C 174 GLU cc_start: 0.8379 (tt0) cc_final: 0.8010 (tp30) REVERT: C 228 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 231 ASN cc_start: 0.8357 (t0) cc_final: 0.7990 (t0) REVERT: D 5 GLU cc_start: 0.8346 (tt0) cc_final: 0.7976 (pt0) REVERT: D 167 LYS cc_start: 0.8928 (tppt) cc_final: 0.8389 (mmmt) REVERT: D 179 ASN cc_start: 0.7930 (m-40) cc_final: 0.7589 (m110) REVERT: D 321 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8392 (tt) REVERT: D 362 TRP cc_start: 0.7627 (t60) cc_final: 0.7252 (t60) REVERT: D 527 ASN cc_start: 0.8510 (t0) cc_final: 0.7936 (t0) REVERT: D 531 MET cc_start: 0.8342 (mtp) cc_final: 0.7929 (mtm) REVERT: D 543 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.6933 (mtm-85) REVERT: D 557 ILE cc_start: 0.9011 (mt) cc_final: 0.8644 (mm) REVERT: D 722 MET cc_start: 0.7744 (ttm) cc_final: 0.7461 (ttm) REVERT: D 841 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7635 (tp) REVERT: D 858 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7705 (mt-10) REVERT: D 939 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6838 (pm20) REVERT: D 958 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8704 (t) REVERT: D 1035 MET cc_start: 0.5999 (ppp) cc_final: 0.5721 (ppp) REVERT: D 1064 LYS cc_start: 0.8264 (mmtm) cc_final: 0.8041 (ttmm) REVERT: D 1073 ARG cc_start: 0.7647 (ttt180) cc_final: 0.7274 (mtp-110) REVERT: D 1115 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7584 (mm) REVERT: D 1132 SER cc_start: 0.8832 (t) cc_final: 0.8446 (m) REVERT: D 1137 MET cc_start: 0.8823 (mtp) cc_final: 0.8539 (mtp) REVERT: D 1185 TYR cc_start: 0.9022 (t80) cc_final: 0.8698 (t80) outliers start: 86 outliers final: 72 residues processed: 380 average time/residue: 0.3494 time to fit residues: 205.2526 Evaluate side-chains 402 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 320 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1090 CYS Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 355 TRP Chi-restraints excluded: chain D residue 487 TYR Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 TRP Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 1004 ILE Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 129 optimal weight: 0.0570 chunk 167 optimal weight: 10.0000 overall best weight: 3.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 808 ASN ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23488 Z= 0.345 Angle : 0.684 9.193 31818 Z= 0.354 Chirality : 0.046 0.258 3436 Planarity : 0.004 0.051 3876 Dihedral : 11.736 165.772 3618 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 3.57 % Allowed : 22.24 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.55 (0.17), residues: 2612 helix: 0.24 (0.16), residues: 1110 sheet: -2.07 (0.33), residues: 250 loop : -2.00 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 178 HIS 0.006 0.001 HIS D 797 PHE 0.016 0.002 PHE B 225 TYR 0.046 0.002 TYR B 258 ARG 0.009 0.001 ARG B1054 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 321 time to evaluate : 2.703 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 148 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8218 (ttmm) REVERT: A 174 GLU cc_start: 0.8358 (tt0) cc_final: 0.8033 (tp30) REVERT: A 231 ASN cc_start: 0.8353 (t0) cc_final: 0.7969 (t0) REVERT: B 5 GLU cc_start: 0.8395 (tt0) cc_final: 0.8179 (tt0) REVERT: B 167 LYS cc_start: 0.8937 (tppt) cc_final: 0.8384 (mmmt) REVERT: B 179 ASN cc_start: 0.7908 (m-40) cc_final: 0.7582 (m110) REVERT: B 321 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8433 (tt) REVERT: B 527 ASN cc_start: 0.8629 (t0) cc_final: 0.7863 (t0) REVERT: B 543 ARG cc_start: 0.7618 (mtm-85) cc_final: 0.7131 (mtm-85) REVERT: B 841 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7644 (tp) REVERT: B 939 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: B 958 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8681 (t) REVERT: B 1033 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7627 (ttm-80) REVERT: B 1035 MET cc_start: 0.5919 (ppp) cc_final: 0.5685 (ppp) REVERT: B 1064 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7853 (ttmm) REVERT: B 1073 ARG cc_start: 0.7720 (ttt180) cc_final: 0.7305 (mtp-110) REVERT: B 1132 SER cc_start: 0.8766 (t) cc_final: 0.8319 (m) REVERT: B 1137 MET cc_start: 0.8935 (mtp) cc_final: 0.8606 (mtp) REVERT: B 1185 TYR cc_start: 0.9132 (t80) cc_final: 0.8624 (t80) REVERT: C 148 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8237 (ttmm) REVERT: C 174 GLU cc_start: 0.8435 (tt0) cc_final: 0.8081 (tp30) REVERT: C 228 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8286 (tm-30) REVERT: C 231 ASN cc_start: 0.8360 (t0) cc_final: 0.7980 (t0) REVERT: D 5 GLU cc_start: 0.8390 (tt0) cc_final: 0.7905 (tt0) REVERT: D 167 LYS cc_start: 0.8936 (tppt) cc_final: 0.8381 (mmmt) REVERT: D 179 ASN cc_start: 0.7918 (m-40) cc_final: 0.7570 (m110) REVERT: D 321 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8434 (tt) REVERT: D 525 PHE cc_start: 0.8686 (m-10) cc_final: 0.8347 (m-10) REVERT: D 526 GLN cc_start: 0.8597 (mt0) cc_final: 0.7923 (mp10) REVERT: D 527 ASN cc_start: 0.8422 (t0) cc_final: 0.7874 (t0) REVERT: D 531 MET cc_start: 0.8415 (mtp) cc_final: 0.7983 (mtm) REVERT: D 543 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.7084 (mtm-85) REVERT: D 557 ILE cc_start: 0.8976 (mt) cc_final: 0.8644 (mm) REVERT: D 722 MET cc_start: 0.7744 (ttm) cc_final: 0.7524 (ttm) REVERT: D 841 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7639 (tp) REVERT: D 939 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: D 958 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8664 (t) REVERT: D 995 TYR cc_start: 0.8855 (m-80) cc_final: 0.8634 (m-10) REVERT: D 1035 MET cc_start: 0.5950 (ppp) cc_final: 0.5712 (ppp) REVERT: D 1064 LYS cc_start: 0.8255 (mmtm) cc_final: 0.8021 (ttmm) REVERT: D 1073 ARG cc_start: 0.7721 (ttt180) cc_final: 0.7304 (mtp-110) REVERT: D 1115 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7600 (mm) REVERT: D 1132 SER cc_start: 0.8771 (t) cc_final: 0.8315 (m) REVERT: D 1137 MET cc_start: 0.8934 (mtp) cc_final: 0.8597 (mtp) REVERT: D 1185 TYR cc_start: 0.9131 (t80) cc_final: 0.8600 (t80) outliers start: 86 outliers final: 72 residues processed: 369 average time/residue: 0.3588 time to fit residues: 208.6844 Evaluate side-chains 390 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 309 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 939 GLU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1086 TRP Chi-restraints excluded: chain B residue 1090 CYS Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 355 TRP Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 TRP Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 939 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 977 THR Chi-restraints excluded: chain D residue 1004 ILE Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1086 TRP Chi-restraints excluded: chain D residue 1090 CYS Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 ASN B 978 ASN ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 ASN ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104054 restraints weight = 40130.830| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.91 r_work: 0.3246 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23488 Z= 0.228 Angle : 0.642 10.023 31818 Z= 0.328 Chirality : 0.044 0.249 3436 Planarity : 0.004 0.051 3876 Dihedral : 11.730 169.008 3618 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.41 % Allowed : 22.90 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.55 (0.17), residues: 2612 helix: 0.22 (0.16), residues: 1124 sheet: -2.11 (0.32), residues: 266 loop : -1.99 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 362 HIS 0.005 0.001 HIS B 797 PHE 0.045 0.001 PHE B 530 TYR 0.032 0.002 TYR B 258 ARG 0.009 0.001 ARG D1054 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5319.16 seconds wall clock time: 97 minutes 41.52 seconds (5861.52 seconds total)