Starting phenix.real_space_refine on Tue Dec 12 22:24:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/12_2023/6nm9_9398.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/12_2023/6nm9_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_9398/12_2023/6nm9_9398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/12_2023/6nm9_9398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/12_2023/6nm9_9398.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nm9_9398/12_2023/6nm9_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 12.18, per 1000 atoms: 0.53 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: 10.44 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: 8.66 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: 8.48 Time building geometry restraints manager: 11.08 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: 13793 33.06 - 66.12: 381 66.12 - 99.19: 40 99.19 - 132.25: 0 132.25 - 165.31: 2 Dihedral angle restraints: 14216 sinusoidal: 6372 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 14213 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: 2.000 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: 4.860 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 69.310 Find NCS groups from input model: 1.260 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.820 ------------------------------------------------------------------------------- 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 : 15.844 165.309 9156 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 : 3.096 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 outliers start: 7 outliers final: 2 residues processed: 458 average time/residue: 0.4146 time to fit residues: 278.2812 Evaluate side-chains 307 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 305 time to evaluate : 2.442 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2064 time to fit residues: 4.1476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 68 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 241 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 808 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 808 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23488 Z= 0.174 Angle : 0.623 11.836 31818 Z= 0.329 Chirality : 0.043 0.253 3436 Planarity : 0.004 0.049 3876 Dihedral : 10.780 171.707 3550 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.75 % Allowed : 16.58 % Favored : 81.67 % 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: -2.85 (0.16), residues: 2612 helix: -0.94 (0.15), residues: 1150 sheet: -2.20 (0.34), residues: 238 loop : -2.80 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 890 HIS 0.003 0.001 HIS A 190 PHE 0.012 0.001 PHE B 315 TYR 0.017 0.001 TYR B 294 ARG 0.008 0.001 ARG D 174 *********************** 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 445 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 403 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 17 residues processed: 431 average time/residue: 0.3841 time to fit residues: 253.8378 Evaluate side-chains 332 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 315 time to evaluate : 2.991 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2439 time to fit residues: 11.5738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.0070 chunk 74 optimal weight: 0.0270 chunk 201 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 241 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 overall best weight: 1.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2477 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= 0.187 Angle : 0.604 12.605 31818 Z= 0.313 Chirality : 0.042 0.240 3436 Planarity : 0.004 0.048 3876 Dihedral : 10.591 170.988 3550 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.12 % Allowed : 17.54 % Favored : 80.34 % 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: -2.20 (0.16), residues: 2612 helix: -0.33 (0.15), residues: 1136 sheet: -1.94 (0.35), residues: 232 loop : -2.48 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 355 HIS 0.003 0.001 HIS D 67 PHE 0.012 0.001 PHE D 109 TYR 0.021 0.001 TYR B 258 ARG 0.004 0.000 ARG B 359 *********************** 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 403 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 352 time to evaluate : 2.656 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 outliers start: 51 outliers final: 26 residues processed: 380 average time/residue: 0.3777 time to fit residues: 219.2811 Evaluate side-chains 324 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 298 time to evaluate : 2.659 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2470 time to fit residues: 14.7830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.0980 chunk 181 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 731 ASN B 732 ASN B 797 HIS ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1172 ASN D 260 ASN D 731 ASN D 732 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** D1172 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23488 Z= 0.188 Angle : 0.584 10.244 31818 Z= 0.304 Chirality : 0.042 0.239 3436 Planarity : 0.003 0.055 3876 Dihedral : 10.572 170.875 3550 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.79 % Allowed : 18.87 % Favored : 79.34 % 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: -1.86 (0.16), residues: 2612 helix: -0.02 (0.16), residues: 1140 sheet: -1.90 (0.35), residues: 240 loop : -2.31 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 362 HIS 0.002 0.001 HIS A 190 PHE 0.011 0.001 PHE D 521 TYR 0.024 0.001 TYR D1185 ARG 0.005 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 383 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 340 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 362 average time/residue: 0.3772 time to fit residues: 209.0699 Evaluate side-chains 312 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 292 time to evaluate : 2.695 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2130 time to fit residues: 11.8236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 219 optimal weight: 0.0370 chunk 177 optimal weight: 0.6980 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: 0.9062 ------------------------------------------------------------------------------- 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 260 ASN D 731 ASN D 797 HIS ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23488 Z= 0.164 Angle : 0.584 9.707 31818 Z= 0.302 Chirality : 0.041 0.230 3436 Planarity : 0.003 0.054 3876 Dihedral : 10.581 172.043 3550 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.25 % Allowed : 20.07 % Favored : 78.68 % 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: -1.60 (0.17), residues: 2612 helix: 0.24 (0.16), residues: 1136 sheet: -1.96 (0.33), residues: 254 loop : -2.16 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 362 HIS 0.003 0.001 HIS B 797 PHE 0.025 0.001 PHE D1027 TYR 0.026 0.001 TYR D1185 ARG 0.005 0.000 ARG D1112 *********************** 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 371 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 341 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 357 average time/residue: 0.3757 time to fit residues: 205.4399 Evaluate side-chains 315 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 299 time to evaluate : 2.542 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2167 time to fit residues: 10.0639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 157 ASN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1172 ASN ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN D1172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23488 Z= 0.263 Angle : 0.626 8.310 31818 Z= 0.326 Chirality : 0.043 0.244 3436 Planarity : 0.004 0.058 3876 Dihedral : 10.707 168.528 3550 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 1.66 % Allowed : 21.36 % Favored : 76.97 % 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: -1.64 (0.17), residues: 2612 helix: 0.20 (0.16), residues: 1144 sheet: -2.14 (0.32), residues: 268 loop : -2.13 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 178 HIS 0.003 0.001 HIS D 797 PHE 0.016 0.001 PHE B 530 TYR 0.044 0.002 TYR B1185 ARG 0.006 0.001 ARG D1033 *********************** 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 355 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 315 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 338 average time/residue: 0.3758 time to fit residues: 197.4994 Evaluate side-chains 317 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 288 time to evaluate : 2.881 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2695 time to fit residues: 17.0686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 146 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** 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: 0.7383 moved from start: 0.3232 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= 0.204 Angle : 0.605 8.884 31818 Z= 0.313 Chirality : 0.042 0.240 3436 Planarity : 0.004 0.058 3876 Dihedral : 10.754 170.287 3550 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.91 % Allowed : 22.57 % Favored : 76.52 % 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: -1.49 (0.17), residues: 2612 helix: 0.34 (0.16), residues: 1130 sheet: -2.12 (0.32), residues: 272 loop : -2.02 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 534 HIS 0.003 0.001 HIS D 797 PHE 0.014 0.001 PHE D 530 TYR 0.043 0.002 TYR D1185 ARG 0.007 0.001 ARG D1054 *********************** 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 332 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 310 time to evaluate : 2.632 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 outliers start: 22 outliers final: 13 residues processed: 325 average time/residue: 0.3631 time to fit residues: 188.6024 Evaluate side-chains 296 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 283 time to evaluate : 2.823 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2193 time to fit residues: 9.0885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1172 ASN ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23488 Z= 0.197 Angle : 0.610 8.205 31818 Z= 0.316 Chirality : 0.042 0.241 3436 Planarity : 0.004 0.056 3876 Dihedral : 10.793 170.448 3550 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.79 % Allowed : 23.40 % Favored : 75.81 % 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: -1.44 (0.17), residues: 2612 helix: 0.38 (0.16), residues: 1126 sheet: -2.22 (0.31), residues: 282 loop : -1.94 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 602 HIS 0.005 0.001 HIS D 759 PHE 0.011 0.001 PHE B 521 TYR 0.040 0.002 TYR D1185 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 322 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 303 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 314 average time/residue: 0.3676 time to fit residues: 181.4628 Evaluate side-chains 300 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 284 time to evaluate : 2.573 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2301 time to fit residues: 10.5006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 ASN ** C 145 ASN ** 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: 0.7373 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23488 Z= 0.199 Angle : 0.627 10.830 31818 Z= 0.321 Chirality : 0.043 0.247 3436 Planarity : 0.004 0.063 3876 Dihedral : 10.795 170.371 3550 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.91 % Allowed : 23.48 % Favored : 75.60 % 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: -1.39 (0.17), residues: 2612 helix: 0.37 (0.16), residues: 1130 sheet: -2.13 (0.31), residues: 276 loop : -1.90 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 534 HIS 0.003 0.001 HIS D 797 PHE 0.024 0.001 PHE D 530 TYR 0.039 0.001 TYR D1185 ARG 0.008 0.001 ARG D1054 *********************** 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 325 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 303 time to evaluate : 2.915 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 outliers start: 22 outliers final: 13 residues processed: 314 average time/residue: 0.3499 time to fit residues: 173.5444 Evaluate side-chains 294 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 281 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2465 time to fit residues: 9.5938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 243 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 129 optimal weight: 0.0030 chunk 167 optimal weight: 7.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1172 ASN C 145 ASN D 853 GLN ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 889 ASN ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23488 Z= 0.246 Angle : 0.658 12.921 31818 Z= 0.338 Chirality : 0.044 0.263 3436 Planarity : 0.004 0.058 3876 Dihedral : 10.845 168.980 3550 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 0.67 % Allowed : 23.90 % Favored : 75.44 % 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: 0.31 (0.16), residues: 1128 sheet: -2.12 (0.31), residues: 284 loop : -1.93 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 534 HIS 0.003 0.001 HIS D 797 PHE 0.016 0.001 PHE D 304 TYR 0.039 0.002 TYR D1185 ARG 0.009 0.001 ARG D1054 ********************** 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 310 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 294 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 302 average time/residue: 0.3504 time to fit residues: 167.2539 Evaluate side-chains 299 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 287 time to evaluate : 2.806 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2301 time to fit residues: 8.8832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 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 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 ASN ** D1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.160391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113835 restraints weight = 40375.060| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.13 r_work: 0.3232 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23488 Z= 0.250 Angle : 0.654 12.095 31818 Z= 0.335 Chirality : 0.044 0.252 3436 Planarity : 0.004 0.052 3876 Dihedral : 10.881 168.825 3550 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.17 % Allowed : 24.77 % Favored : 75.06 % 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: -1.49 (0.17), residues: 2612 helix: 0.30 (0.16), residues: 1130 sheet: -2.09 (0.31), residues: 290 loop : -1.96 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 534 HIS 0.003 0.001 HIS B 797 PHE 0.014 0.001 PHE D1027 TYR 0.038 0.002 TYR D1185 ARG 0.009 0.001 ARG B1054 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5099.03 seconds wall clock time: 93 minutes 54.10 seconds (5634.10 seconds total)