Starting phenix.real_space_refine (version: dev) on Wed Feb 22 08:15:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/02_2023/6iqw_9708_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/02_2023/6iqw_9708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/02_2023/6iqw_9708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/02_2023/6iqw_9708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/02_2023/6iqw_9708_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/02_2023/6iqw_9708_updated.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 1.289 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 Process input model Symmetric amino acids flipped Residue "A ARG 385": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "E TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16935 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6131 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1094 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "C" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2113 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2106 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2177 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 510 Classifications: {'RNA': 24} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna2p': 11, 'rna3p': 12} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.90, per 1000 atoms: 0.58 Number of scatterers: 16935 At special positions: 0 Unit cell: (134.16, 147.68, 108.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 26 15.00 O 3146 8.00 N 2947 7.00 C 10766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 274 " distance=2.04 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: 7.73 Conformation dependent library (CDL) restraints added in 2.6 seconds 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 14 sheets defined 34.3% alpha, 6.5% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.898A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.599A pdb=" N ALA A 23 " --> pdb=" O PRO A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.636A pdb=" N GLY A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.990A pdb=" N LEU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 removed outlier: 3.780A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 87 through 103 removed outlier: 4.072A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.808A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Proline residue: A 177 - end of helix removed outlier: 3.672A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 213 Processing helix chain 'A' and resid 219 through 222 No H-bonds generated for 'chain 'A' and resid 219 through 222' Processing helix chain 'A' and resid 244 through 247 No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 256 through 281 removed outlier: 3.726A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 340 through 343 removed outlier: 3.502A pdb=" N PHE A 343 " --> pdb=" O GLY A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 351 through 368 Processing helix chain 'A' and resid 414 through 426 removed outlier: 3.698A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 4.060A pdb=" N MET A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 551 removed outlier: 3.843A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 562 through 565 No H-bonds generated for 'chain 'A' and resid 562 through 565' Processing helix chain 'A' and resid 596 through 613 removed outlier: 3.988A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 649 removed outlier: 4.107A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 removed outlier: 3.855A pdb=" N GLU A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 688 No H-bonds generated for 'chain 'A' and resid 685 through 688' Processing helix chain 'A' and resid 705 through 718 removed outlier: 3.591A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 711 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.780A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A 735 " --> pdb=" O TYR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 746 No H-bonds generated for 'chain 'A' and resid 743 through 746' Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 765 through 772 removed outlier: 4.442A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 71 through 87 removed outlier: 4.072A pdb=" N LEU B 75 " --> pdb=" O PRO B 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 removed outlier: 4.426A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.565A pdb=" N MET B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 156 removed outlier: 3.875A pdb=" N ARG B 147 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 148 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 149 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP B 150 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.895A pdb=" N GLU B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 155 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 156 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.971A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.910A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 128 No H-bonds generated for 'chain 'C' and resid 125 through 128' Processing helix chain 'C' and resid 150 through 158 removed outlier: 3.621A pdb=" N GLU C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 219 Processing helix chain 'C' and resid 249 through 252 No H-bonds generated for 'chain 'C' and resid 249 through 252' Processing helix chain 'C' and resid 268 through 271 No H-bonds generated for 'chain 'C' and resid 268 through 271' Processing helix chain 'C' and resid 277 through 286 removed outlier: 4.934A pdb=" N GLU C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 70 removed outlier: 3.629A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.671A pdb=" N ASN D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 128 No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 150 through 157 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 207 through 222 removed outlier: 3.898A pdb=" N LYS D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 248 through 251 No H-bonds generated for 'chain 'D' and resid 248 through 251' Processing helix chain 'D' and resid 271 through 277 removed outlier: 4.361A pdb=" N SER D 274 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 276 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 34 Processing helix chain 'E' and resid 46 through 49 No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 77 through 83 removed outlier: 4.176A pdb=" N THR E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY E 83 " --> pdb=" O GLY E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 96 removed outlier: 3.521A pdb=" N ALA E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 172 through 178 removed outlier: 4.169A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 45 Processing helix chain 'F' and resid 65 through 70 Processing helix chain 'F' and resid 114 through 133 removed outlier: 3.984A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 143 removed outlier: 3.554A pdb=" N MET F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 154 removed outlier: 3.792A pdb=" N ASP F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 181 through 187 Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 205 through 208 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 257 through 260 No H-bonds generated for 'chain 'F' and resid 257 through 260' Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 281 through 304 removed outlier: 3.626A pdb=" N PHE F 285 " --> pdb=" O PRO F 281 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR F 298 " --> pdb=" O ASP F 294 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET F 301 " --> pdb=" O TYR F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 322 Processing sheet with id= A, first strand: chain 'A' and resid 330 through 336 removed outlier: 3.767A pdb=" N PHE A 290 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 299 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL A 288 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 450 through 454 removed outlier: 3.968A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN A 481 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 467 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 483 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 620 through 627 removed outlier: 4.058A pdb=" N PHE A 590 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 589 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 593 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL A 582 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA A 595 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 580 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 9 through 13 Processing sheet with id= E, first strand: chain 'C' and resid 15 through 17 Processing sheet with id= F, first strand: chain 'C' and resid 167 through 169 Processing sheet with id= G, first strand: chain 'D' and resid 9 through 11 Processing sheet with id= H, first strand: chain 'D' and resid 167 through 169 Processing sheet with id= I, first strand: chain 'E' and resid 157 through 161 removed outlier: 3.567A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 3 through 6 Processing sheet with id= K, first strand: chain 'F' and resid 209 through 211 Processing sheet with id= L, first strand: chain 'F' and resid 222 through 227 removed outlier: 4.706A pdb=" N ILE F 238 " --> pdb=" O VAL F 227 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 331 through 334 Processing sheet with id= N, first strand: chain 'F' and resid 33 through 35 removed outlier: 3.887A pdb=" N TYR F 85 " --> pdb=" O VAL F 34 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 8.24 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: 3929 1.33 - 1.45: 3922 1.45 - 1.57: 9395 1.57 - 1.69: 51 1.69 - 1.82: 82 Bond restraints: 17379 Sorted by residual: bond pdb=" C LEU F 20 " pdb=" N THR F 21 " ideal model delta sigma weight residual 1.331 1.207 0.124 1.59e-02 3.96e+03 6.11e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.65e+01 bond pdb=" N ARG E 89 " pdb=" CA ARG E 89 " ideal model delta sigma weight residual 1.459 1.400 0.059 1.16e-02 7.43e+03 2.56e+01 bond pdb=" C5 ATP A 801 " pdb=" N7 ATP A 801 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.48e+01 ... (remaining 17374 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.60: 495 105.60 - 113.18: 9201 113.18 - 120.76: 8284 120.76 - 128.34: 5456 128.34 - 135.92: 179 Bond angle restraints: 23615 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 120.83 19.04 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 119.70 17.13 1.00e+00 1.00e+00 2.93e+02 angle pdb=" C GLU E 88 " pdb=" N ARG E 89 " pdb=" CA ARG E 89 " ideal model delta sigma weight residual 120.79 108.58 12.21 1.39e+00 5.18e-01 7.71e+01 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.56 8.24 1.00e+00 1.00e+00 6.79e+01 angle pdb=" N3 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N9 ATP A 801 " ideal model delta sigma weight residual 127.04 135.05 -8.01 1.15e+00 7.59e-01 4.87e+01 ... (remaining 23610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.01: 9052 19.01 - 38.02: 1053 38.02 - 57.03: 174 57.03 - 76.03: 25 76.03 - 95.04: 2 Dihedral angle restraints: 10306 sinusoidal: 4363 harmonic: 5943 Sorted by residual: dihedral pdb=" CA PHE A 325 " pdb=" C PHE A 325 " pdb=" N GLU A 326 " pdb=" CA GLU A 326 " ideal model delta harmonic sigma weight residual -180.00 -145.33 -34.67 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA VAL D 39 " pdb=" C VAL D 39 " pdb=" N ILE D 40 " pdb=" CA ILE D 40 " ideal model delta harmonic sigma weight residual -180.00 -146.38 -33.62 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA ARG A 394 " pdb=" C ARG A 394 " pdb=" N GLU A 395 " pdb=" CA GLU A 395 " ideal model delta harmonic sigma weight residual 180.00 146.74 33.26 0 5.00e+00 4.00e-02 4.43e+01 ... (remaining 10303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1886 0.060 - 0.119: 548 0.119 - 0.179: 119 0.179 - 0.238: 14 0.238 - 0.298: 4 Chirality restraints: 2571 Sorted by residual: chirality pdb=" C1' A I 18 " pdb=" O4' A I 18 " pdb=" C2' A I 18 " pdb=" N9 A I 18 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE D 196 " pdb=" CA ILE D 196 " pdb=" CG1 ILE D 196 " pdb=" CG2 ILE D 196 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE C 15 " pdb=" CA ILE C 15 " pdb=" CG1 ILE C 15 " pdb=" CG2 ILE C 15 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2568 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 141 " -0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C SER E 141 " 0.068 2.00e-02 2.50e+03 pdb=" O SER E 141 " -0.025 2.00e-02 2.50e+03 pdb=" N SER E 142 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 58 " 0.059 5.00e-02 4.00e+02 8.96e-02 1.28e+01 pdb=" N PRO E 59 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 59 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 59 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 494 " -0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 495 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " -0.046 5.00e-02 4.00e+02 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 48 2.39 - 3.01: 8742 3.01 - 3.64: 26097 3.64 - 4.27: 38714 4.27 - 4.90: 62731 Nonbonded interactions: 136332 Sorted by model distance: nonbonded pdb=" O ALA B 51 " pdb=" CD2 TYR B 55 " model vdw 1.757 3.340 nonbonded pdb=" O ARG E 89 " pdb=" OG1 THR E 92 " model vdw 2.168 2.440 nonbonded pdb=" O GLY F 15 " pdb=" O2' C I 21 " model vdw 2.210 2.440 nonbonded pdb=" O GLU E 88 " pdb=" O ARG E 89 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR A 727 " pdb=" O GLN B 173 " model vdw 2.254 2.440 ... (remaining 136327 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 'C' and (resid 4 through 25 or resid 38 through 194 or (resid 195 and (na \ me N or name CA or name C or name O or name CB )) or resid 196 through 282)) selection = (chain 'D' and (resid 4 through 25 or resid 38 through 63 or (resid 64 and (name \ N or name CA or name C or name O or name CB )) or resid 65 through 223 or (resi \ d 224 and (name N or name CA or name C or name O or name CB )) or resid 225 thro \ ugh 234 or (resid 235 and (name N or name CA or name C or name O or name CB )) o \ r resid 236 through 282)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 50 5.16 5 C 10766 2.51 5 N 2947 2.21 5 O 3146 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.660 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: 0.010 Extract box with map and model: 4.470 Check model and map are aligned: 0.260 Process input model: 47.320 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 0.007 0.124 17379 Z= 0.445 Angle : 1.051 19.035 23615 Z= 0.594 Chirality : 0.059 0.298 2571 Planarity : 0.008 0.090 2941 Dihedral : 15.757 95.044 6507 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.52 % Favored : 86.09 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.25 % 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: -4.93 (0.14), residues: 2049 helix: -3.21 (0.12), residues: 730 sheet: -3.15 (0.34), residues: 185 loop : -3.44 (0.16), residues: 1134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 678 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 680 average time/residue: 0.3211 time to fit residues: 317.6875 Evaluate side-chains 459 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 456 time to evaluate : 1.829 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3363 time to fit residues: 3.9897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 162 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 0.0970 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN A 194 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 205 HIS ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 17379 Z= 0.238 Angle : 0.737 11.670 23615 Z= 0.382 Chirality : 0.048 0.310 2571 Planarity : 0.006 0.080 2941 Dihedral : 9.571 94.863 2583 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.05 % Favored : 87.70 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.16), residues: 2049 helix: -1.83 (0.16), residues: 740 sheet: -2.50 (0.34), residues: 200 loop : -3.18 (0.17), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 487 time to evaluate : 1.925 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 outliers start: 73 outliers final: 54 residues processed: 528 average time/residue: 0.3071 time to fit residues: 242.0881 Evaluate side-chains 484 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 430 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.1672 time to fit residues: 19.2581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 156 optimal weight: 0.0170 chunk 128 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 17379 Z= 0.234 Angle : 0.704 11.487 23615 Z= 0.364 Chirality : 0.047 0.294 2571 Planarity : 0.006 0.085 2941 Dihedral : 9.233 93.023 2583 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.10 % Favored : 87.75 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.17), residues: 2049 helix: -1.22 (0.18), residues: 742 sheet: -2.63 (0.33), residues: 207 loop : -3.00 (0.17), residues: 1100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 470 time to evaluate : 1.818 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 outliers start: 43 outliers final: 22 residues processed: 492 average time/residue: 0.2909 time to fit residues: 214.5315 Evaluate side-chains 448 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 426 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1496 time to fit residues: 8.8278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 179 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS C 183 ASN E 30 ASN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 17379 Z= 0.225 Angle : 0.690 12.488 23615 Z= 0.353 Chirality : 0.047 0.274 2571 Planarity : 0.005 0.076 2941 Dihedral : 9.017 90.573 2583 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.35 % Favored : 87.51 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.17), residues: 2049 helix: -0.89 (0.18), residues: 749 sheet: -2.56 (0.33), residues: 211 loop : -2.86 (0.18), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 452 time to evaluate : 1.938 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 outliers start: 61 outliers final: 34 residues processed: 479 average time/residue: 0.2847 time to fit residues: 207.0777 Evaluate side-chains 439 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 405 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1838 time to fit residues: 13.6973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 179 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS F 46 ASN F 90 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 17379 Z= 0.302 Angle : 0.717 13.235 23615 Z= 0.370 Chirality : 0.048 0.263 2571 Planarity : 0.006 0.071 2941 Dihedral : 8.947 87.151 2583 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.59 % Favored : 87.21 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2049 helix: -0.68 (0.18), residues: 751 sheet: -2.42 (0.34), residues: 212 loop : -2.75 (0.18), residues: 1086 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 426 time to evaluate : 1.779 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 outliers start: 54 outliers final: 36 residues processed: 448 average time/residue: 0.2914 time to fit residues: 198.8570 Evaluate side-chains 436 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 400 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1684 time to fit residues: 14.1240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 49 optimal weight: 0.0970 chunk 200 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 92 optimal weight: 0.0770 chunk 16 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 overall best weight: 3.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 17379 Z= 0.260 Angle : 0.698 14.171 23615 Z= 0.355 Chirality : 0.047 0.251 2571 Planarity : 0.005 0.067 2941 Dihedral : 8.817 84.587 2583 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.35 % Favored : 87.51 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.71 (0.18), residues: 2049 helix: -0.57 (0.18), residues: 762 sheet: -2.25 (0.35), residues: 207 loop : -2.70 (0.18), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 430 time to evaluate : 1.959 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 outliers start: 46 outliers final: 31 residues processed: 450 average time/residue: 0.2915 time to fit residues: 198.1614 Evaluate side-chains 432 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 401 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1731 time to fit residues: 12.5608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.0980 chunk 22 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 0.0980 chunk 111 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17379 Z= 0.210 Angle : 0.695 14.135 23615 Z= 0.350 Chirality : 0.047 0.234 2571 Planarity : 0.005 0.065 2941 Dihedral : 8.719 83.709 2583 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.96 % Favored : 87.95 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.18), residues: 2049 helix: -0.48 (0.18), residues: 763 sheet: -2.13 (0.36), residues: 198 loop : -2.60 (0.18), residues: 1088 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 439 time to evaluate : 1.964 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 outliers start: 21 outliers final: 15 residues processed: 447 average time/residue: 0.2890 time to fit residues: 195.4798 Evaluate side-chains 423 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 408 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1600 time to fit residues: 7.2929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 overall best weight: 1.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 HIS ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 17379 Z= 0.209 Angle : 0.699 15.065 23615 Z= 0.349 Chirality : 0.047 0.237 2571 Planarity : 0.005 0.063 2941 Dihedral : 8.683 82.734 2583 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.52 % Favored : 88.38 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.55 (0.18), residues: 2049 helix: -0.47 (0.18), residues: 765 sheet: -2.22 (0.37), residues: 189 loop : -2.58 (0.18), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 428 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 442 average time/residue: 0.2835 time to fit residues: 192.4059 Evaluate side-chains 417 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 398 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1817 time to fit residues: 9.2325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.0370 chunk 191 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 168 optimal weight: 0.0000 chunk 175 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.8068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 HIS ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 17379 Z= 0.252 Angle : 0.739 13.004 23615 Z= 0.368 Chirality : 0.048 0.262 2571 Planarity : 0.005 0.067 2941 Dihedral : 8.670 82.180 2583 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.35 % Favored : 87.55 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.18), residues: 2049 helix: -0.35 (0.19), residues: 746 sheet: -2.25 (0.36), residues: 192 loop : -2.51 (0.18), residues: 1111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 409 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 410 average time/residue: 0.2807 time to fit residues: 177.1692 Evaluate side-chains 399 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 387 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1824 time to fit residues: 6.9477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 126 optimal weight: 0.0970 chunk 100 optimal weight: 0.0970 chunk 130 optimal weight: 2.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 17379 Z= 0.197 Angle : 0.745 13.793 23615 Z= 0.364 Chirality : 0.047 0.258 2571 Planarity : 0.005 0.067 2941 Dihedral : 8.589 81.180 2583 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.59 % Favored : 89.36 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.18), residues: 2049 helix: -0.26 (0.19), residues: 729 sheet: -2.10 (0.38), residues: 184 loop : -2.37 (0.18), residues: 1136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 438 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 443 average time/residue: 0.2882 time to fit residues: 194.6714 Evaluate side-chains 408 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 399 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1823 time to fit residues: 5.7097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS C 44 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.144853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119405 restraints weight = 33243.973| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.04 r_work: 0.3441 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 17379 Z= 0.259 Angle : 0.749 12.749 23615 Z= 0.374 Chirality : 0.048 0.268 2571 Planarity : 0.006 0.075 2941 Dihedral : 8.629 82.766 2583 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.66 % Favored : 88.24 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.28 (0.18), residues: 2049 helix: -0.20 (0.19), residues: 735 sheet: -2.21 (0.38), residues: 179 loop : -2.38 (0.18), residues: 1135 =============================================================================== Job complete usr+sys time: 4217.88 seconds wall clock time: 76 minutes 45.01 seconds (4605.01 seconds total)