Starting phenix.real_space_refine on Sun Dec 10 19:21:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/12_2023/8d37_27155_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/12_2023/8d37_27155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/12_2023/8d37_27155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/12_2023/8d37_27155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/12_2023/8d37_27155_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/12_2023/8d37_27155_neut_updated.pdb" } resolution = 2.65 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= 0.339 sd= 0.592 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 Ca 1 9.91 5 P 51 5.49 5 S 82 5.16 5 C 9605 2.51 5 N 2690 2.21 5 O 2885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7778 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 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: "B" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3307 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3213 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.30, per 1000 atoms: 0.54 Number of scatterers: 15314 At special positions: 0 Unit cell: (113.05, 112.2, 153, 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) Ca 1 19.99 S 82 16.00 P 51 15.00 O 2885 8.00 N 2690 7.00 C 9605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " 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: 6.04 Conformation dependent library (CDL) restraints added in 2.6 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 10 sheets defined 42.8% alpha, 13.7% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 6.64 Creating SS restraints... Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 135 through 158 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.787A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 removed outlier: 3.564A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 389 through 417 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.534A pdb=" N ALA A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 481 removed outlier: 3.703A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 475 " --> pdb=" O CYS A 471 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.636A pdb=" N ASP A 542 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET A 544 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 547 " --> pdb=" O MET A 544 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 551 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 553 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.722A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 649 through 662 removed outlier: 3.797A pdb=" N LEU A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 Proline residue: A 772 - end of helix Processing helix chain 'A' and resid 787 through 809 removed outlier: 4.950A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.516A pdb=" N LEU A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 959 through 969 removed outlier: 3.514A pdb=" N PHE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 989 Processing helix chain 'A' and resid 1055 through 1066 Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1085 through 1088 No H-bonds generated for 'chain 'A' and resid 1085 through 1088' Processing helix chain 'A' and resid 1093 through 1122 removed outlier: 3.617A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1168 removed outlier: 4.520A pdb=" N TYR A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1205 through 1208 No H-bonds generated for 'chain 'A' and resid 1205 through 1208' Processing helix chain 'A' and resid 1220 through 1227 Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.355A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 removed outlier: 4.573A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 266 removed outlier: 3.926A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 392 through 409 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 425 through 434 Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 468 through 484 removed outlier: 4.447A pdb=" N LYS B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 151 through 154 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.635A pdb=" N GLU C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 177 " --> pdb=" O ASN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 removed outlier: 4.352A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 266 removed outlier: 4.495A pdb=" N ASN C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLN C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 319 through 322 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 392 through 409 removed outlier: 3.559A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 425 through 434 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.633A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 484 removed outlier: 4.256A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 482 " --> pdb=" O TYR C 478 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.936A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER A 216 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ALA A 194 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU A 265 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE A 197 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 267 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N VAL A 199 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 290 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLY A 268 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 292 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 435 through 438 Processing sheet with id= C, first strand: chain 'A' and resid 612 through 615 removed outlier: 6.842A pdb=" N GLY A 746 " --> pdb=" O GLY A 626 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1216 through 1218 removed outlier: 5.591A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.737A pdb=" N GLY B 207 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 307 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER B 337 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN B 305 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN B 339 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 303 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASP B 341 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU B 301 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 289 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR B 302 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 287 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 323 through 326 Processing sheet with id= G, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.939A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE B 439 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ASP B 386 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 441 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.928A pdb=" N GLY C 207 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 307 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER C 337 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN C 305 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN C 339 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU C 303 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP C 341 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU C 301 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU C 289 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR C 302 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN C 287 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TRP C 304 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS C 285 " --> pdb=" O TRP C 304 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 323 through 326 Processing sheet with id= J, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.273A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE C 439 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ASP C 386 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C 441 " --> pdb=" O ASP C 386 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 6.03 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4753 1.34 - 1.46: 2701 1.46 - 1.58: 8119 1.58 - 1.70: 95 1.70 - 1.82: 130 Bond restraints: 15798 Sorted by residual: bond pdb=" O5' DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.579 1.799 -0.220 1.50e-02 4.44e+03 2.16e+02 bond pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.592 1.706 -0.114 1.10e-02 8.26e+03 1.08e+02 bond pdb=" C5' DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 1.443 1.329 0.114 1.10e-02 8.26e+03 1.08e+02 bond pdb=" C4' DCP A1302 " pdb=" C5' DCP A1302 " ideal model delta sigma weight residual 1.508 1.560 -0.052 1.10e-02 8.26e+03 2.25e+01 bond pdb=" C4 DCP A1302 " pdb=" N4 DCP A1302 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.20e-02 6.94e+03 2.08e+01 ... (remaining 15793 not shown) Histogram of bond angle deviations from ideal: 91.12 - 99.84: 5 99.84 - 108.55: 1392 108.55 - 117.27: 10293 117.27 - 125.99: 9414 125.99 - 134.71: 516 Bond angle restraints: 21620 Sorted by residual: angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 133.36 6.51 1.00e+00 1.00e+00 4.24e+01 angle pdb=" O2G DCP A1302 " pdb=" PG DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 104.48 97.88 6.60 1.14e+00 7.76e-01 3.38e+01 angle pdb=" O2A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " ideal model delta sigma weight residual 106.94 116.91 -9.97 1.88e+00 2.83e-01 2.81e+01 angle pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 101.57 93.68 7.89 1.54e+00 4.24e-01 2.64e+01 angle pdb=" O3A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 102.67 91.12 11.55 2.38e+00 1.77e-01 2.36e+01 ... (remaining 21615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 8632 17.05 - 34.10: 477 34.10 - 51.15: 128 51.15 - 68.20: 69 68.20 - 85.25: 6 Dihedral angle restraints: 9312 sinusoidal: 4165 harmonic: 5147 Sorted by residual: dihedral pdb=" CA ASP B 159 " pdb=" C ASP B 159 " pdb=" N LYS B 160 " pdb=" CA LYS B 160 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LYS C 164 " pdb=" C LYS C 164 " pdb=" N GLU C 165 " pdb=" CA GLU C 165 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 125.77 -32.77 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 9309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1619 0.031 - 0.062: 479 0.062 - 0.094: 133 0.094 - 0.125: 90 0.125 - 0.156: 9 Chirality restraints: 2330 Sorted by residual: chirality pdb=" C4' DCP A1302 " pdb=" C3' DCP A1302 " pdb=" C5' DCP A1302 " pdb=" O4' DCP A1302 " both_signs ideal model delta sigma weight residual False -2.50 -2.66 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA VAL B 443 " pdb=" N VAL B 443 " pdb=" C VAL B 443 " pdb=" CB VAL B 443 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2327 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 435 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO A 436 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1199 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A1200 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A1200 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1200 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG P 8 " 0.017 2.00e-02 2.50e+03 6.96e-03 1.45e+00 pdb=" N9 DG P 8 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG P 8 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG P 8 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG P 8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG P 8 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG P 8 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG P 8 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG P 8 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG P 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG P 8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG P 8 " -0.002 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 121 2.55 - 3.14: 12211 3.14 - 3.72: 23830 3.72 - 4.31: 33483 4.31 - 4.90: 54695 Nonbonded interactions: 124340 Sorted by model distance: nonbonded pdb=" OD1 ASP A 904 " pdb=" OG1 THR A 914 " model vdw 1.962 2.440 nonbonded pdb=" OE1 GLU A 895 " pdb=" OH TYR A 955 " model vdw 2.040 2.440 nonbonded pdb=" NZ LYS A 461 " pdb=" O LYS B 265 " model vdw 2.130 2.520 nonbonded pdb=" O MET C 435 " pdb=" OG SER C 436 " model vdw 2.137 2.440 nonbonded pdb=" O THR B 460 " pdb=" OG1 THR B 461 " model vdw 2.165 2.440 ... (remaining 124335 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 'B' and (resid 67 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 355 or resid 368 through 485)) selection = chain 'C' } 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: 2.740 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: 7.940 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 46.180 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.003 0.220 15798 Z= 0.178 Angle : 0.519 12.913 21620 Z= 0.289 Chirality : 0.037 0.156 2330 Planarity : 0.003 0.037 2604 Dihedral : 12.722 85.251 5987 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.32 % Allowed : 2.07 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1758 helix: 1.14 (0.21), residues: 713 sheet: 0.81 (0.32), residues: 240 loop : 0.24 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.003 0.001 HIS A 138 PHE 0.011 0.001 PHE A 197 TYR 0.009 0.001 TYR A1108 ARG 0.003 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 524 time to evaluate : 1.895 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: 5 outliers final: 3 residues processed: 528 average time/residue: 1.2010 time to fit residues: 700.6551 Evaluate side-chains 398 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 395 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1758 time to fit residues: 2.3480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A1059 ASN A1098 ASN A1110 HIS B 124 GLN B 132 HIS B 216 HIS B 397 GLN C 85 GLN C 258 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 15798 Z= 0.469 Angle : 0.800 9.965 21620 Z= 0.414 Chirality : 0.051 0.257 2330 Planarity : 0.007 0.064 2604 Dihedral : 15.047 89.597 2478 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.72 % Allowed : 13.05 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1758 helix: 0.50 (0.19), residues: 720 sheet: 0.36 (0.30), residues: 242 loop : -0.36 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 918 HIS 0.009 0.002 HIS C 187 PHE 0.022 0.003 PHE B 219 TYR 0.022 0.003 TYR B 291 ARG 0.010 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 385 time to evaluate : 1.649 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: 104 outliers final: 54 residues processed: 442 average time/residue: 1.1685 time to fit residues: 574.2026 Evaluate side-chains 428 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 374 time to evaluate : 1.631 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 34 residues processed: 20 average time/residue: 0.3459 time to fit residues: 11.8702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 163 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 468 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 922 GLN A 968 GLN A1110 HIS B 124 GLN B 287 ASN C 85 GLN C 258 HIS C 339 ASN C 400 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15798 Z= 0.300 Angle : 0.673 9.355 21620 Z= 0.352 Chirality : 0.044 0.162 2330 Planarity : 0.006 0.048 2604 Dihedral : 15.048 87.878 2478 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.72 % Allowed : 15.96 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1758 helix: 0.68 (0.19), residues: 710 sheet: 0.50 (0.31), residues: 238 loop : -0.49 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 241 HIS 0.006 0.001 HIS B 77 PHE 0.018 0.002 PHE B 403 TYR 0.014 0.002 TYR B 206 ARG 0.005 0.001 ARG A 993 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 389 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 59 residues processed: 438 average time/residue: 1.1880 time to fit residues: 577.8409 Evaluate side-chains 433 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 374 time to evaluate : 1.619 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 35 residues processed: 24 average time/residue: 0.6138 time to fit residues: 20.0065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 0.0060 chunk 110 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 736 ASN A 758 ASN A 922 GLN A1110 HIS B 124 GLN B 184 ASN B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15798 Z= 0.188 Angle : 0.601 10.302 21620 Z= 0.312 Chirality : 0.040 0.144 2330 Planarity : 0.005 0.052 2604 Dihedral : 14.858 79.790 2478 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.14 % Allowed : 18.02 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1758 helix: 1.08 (0.20), residues: 705 sheet: 0.81 (0.32), residues: 225 loop : -0.40 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 241 HIS 0.004 0.001 HIS A 138 PHE 0.013 0.001 PHE C 273 TYR 0.017 0.001 TYR B 432 ARG 0.006 0.000 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 393 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 51 residues processed: 443 average time/residue: 1.1734 time to fit residues: 578.0680 Evaluate side-chains 429 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 378 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 34 residues processed: 17 average time/residue: 0.3727 time to fit residues: 10.5383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 0.0060 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15798 Z= 0.259 Angle : 0.650 11.264 21620 Z= 0.336 Chirality : 0.042 0.179 2330 Planarity : 0.005 0.049 2604 Dihedral : 14.952 77.635 2478 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.85 % Allowed : 19.12 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1758 helix: 0.89 (0.20), residues: 715 sheet: 0.56 (0.31), residues: 243 loop : -0.51 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 490 HIS 0.006 0.001 HIS A 565 PHE 0.017 0.002 PHE C 273 TYR 0.022 0.002 TYR C 315 ARG 0.014 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 382 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 63 residues processed: 436 average time/residue: 1.1385 time to fit residues: 553.1795 Evaluate side-chains 435 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 372 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 38 residues processed: 26 average time/residue: 0.2641 time to fit residues: 12.2131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 175 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 81 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 264 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15798 Z= 0.156 Angle : 0.595 13.399 21620 Z= 0.303 Chirality : 0.040 0.190 2330 Planarity : 0.004 0.048 2604 Dihedral : 14.711 73.932 2478 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.23 % Allowed : 20.99 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1758 helix: 1.25 (0.20), residues: 710 sheet: 0.88 (0.33), residues: 229 loop : -0.37 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 241 HIS 0.005 0.001 HIS A 565 PHE 0.013 0.001 PHE A 197 TYR 0.019 0.001 TYR B 432 ARG 0.008 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 393 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 42 residues processed: 447 average time/residue: 1.2043 time to fit residues: 600.6348 Evaluate side-chains 413 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 371 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 32 residues processed: 11 average time/residue: 0.4737 time to fit residues: 9.0162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 0.0170 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 0.2980 chunk 80 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15798 Z= 0.186 Angle : 0.615 13.628 21620 Z= 0.312 Chirality : 0.040 0.175 2330 Planarity : 0.005 0.065 2604 Dihedral : 14.679 73.173 2478 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.78 % Allowed : 21.96 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1758 helix: 1.25 (0.20), residues: 710 sheet: 0.94 (0.34), residues: 222 loop : -0.27 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 241 HIS 0.004 0.001 HIS A 565 PHE 0.022 0.001 PHE C 273 TYR 0.023 0.002 TYR A 479 ARG 0.014 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 374 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 46 residues processed: 419 average time/residue: 1.1793 time to fit residues: 551.7687 Evaluate side-chains 406 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 360 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 11 average time/residue: 0.3106 time to fit residues: 7.1992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN C 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15798 Z= 0.339 Angle : 0.726 15.014 21620 Z= 0.372 Chirality : 0.045 0.188 2330 Planarity : 0.006 0.085 2604 Dihedral : 15.051 72.674 2478 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.56 % Allowed : 22.22 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1758 helix: 0.71 (0.19), residues: 724 sheet: 0.69 (0.33), residues: 222 loop : -0.56 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 490 HIS 0.006 0.001 HIS A1110 PHE 0.018 0.002 PHE C 273 TYR 0.021 0.003 TYR A 479 ARG 0.017 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 371 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 63 residues processed: 416 average time/residue: 1.1659 time to fit residues: 540.3318 Evaluate side-chains 427 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 364 time to evaluate : 1.636 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 40 residues processed: 23 average time/residue: 0.4367 time to fit residues: 15.1294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 171 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 GLN A 968 GLN A1110 HIS A1157 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 366 ASN C 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15798 Z= 0.245 Angle : 0.686 17.906 21620 Z= 0.346 Chirality : 0.043 0.190 2330 Planarity : 0.005 0.088 2604 Dihedral : 14.968 72.454 2478 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.07 % Allowed : 24.22 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1758 helix: 0.77 (0.20), residues: 720 sheet: 0.58 (0.33), residues: 233 loop : -0.53 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 490 HIS 0.005 0.001 HIS B 454 PHE 0.016 0.002 PHE C 273 TYR 0.020 0.002 TYR A 479 ARG 0.018 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 365 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 51 residues processed: 409 average time/residue: 1.1910 time to fit residues: 541.8281 Evaluate side-chains 408 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 357 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 39 residues processed: 12 average time/residue: 0.5959 time to fit residues: 11.2146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 chunk 180 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 GLN A 968 GLN A1110 HIS A1157 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN C 258 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15798 Z= 0.207 Angle : 0.671 17.049 21620 Z= 0.336 Chirality : 0.042 0.173 2330 Planarity : 0.005 0.088 2604 Dihedral : 14.859 72.431 2478 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.49 % Allowed : 24.61 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1758 helix: 0.96 (0.20), residues: 713 sheet: 0.79 (0.34), residues: 219 loop : -0.43 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 490 HIS 0.004 0.001 HIS A 565 PHE 0.018 0.002 PHE C 254 TYR 0.021 0.002 TYR C 315 ARG 0.019 0.001 ARG A 650 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 362 time to evaluate : 1.724 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: 54 outliers final: 44 residues processed: 404 average time/residue: 1.1765 time to fit residues: 530.3148 Evaluate side-chains 395 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 351 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 37 residues processed: 7 average time/residue: 0.8591 time to fit residues: 9.2851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.0070 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 147 optimal weight: 0.0040 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.0060 chunk 126 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.1426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 GLN A1059 ASN A1110 HIS A1157 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 404 ASN ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.150527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.140653 restraints weight = 29376.344| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.77 r_work: 0.3924 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 0.044 15798 Z= 0.163 Angle : 0.648 17.410 21620 Z= 0.322 Chirality : 0.040 0.225 2330 Planarity : 0.005 0.066 2604 Dihedral : 14.597 74.421 2478 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.17 % Allowed : 25.52 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1758 helix: 1.28 (0.20), residues: 711 sheet: 1.05 (0.34), residues: 219 loop : -0.22 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 175 HIS 0.008 0.001 HIS A 565 PHE 0.018 0.001 PHE B 219 TYR 0.016 0.001 TYR C 429 ARG 0.017 0.001 ARG A 650 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8145.74 seconds wall clock time: 143 minutes 40.83 seconds (8620.83 seconds total)