Starting phenix.real_space_refine on Sat Sep 12 06:51:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tz1_20586/09_2026/6tz1_20586.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tz1_20586/09_2026/6tz1_20586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6tz1_20586/09_2026/6tz1_20586.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tz1_20586/09_2026/6tz1_20586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tz1_20586/09_2026/6tz1_20586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tz1_20586/09_2026/6tz1_20586.map" model { file = "/net/cci-nas-00/data/ceres_data/6tz1_20586/09_2026/6tz1_20586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tz1_20586/09_2026/6tz1_20586.cif" } resolution = 3.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 54 5.16 5 C 8949 2.51 5 N 2428 2.21 5 O 2755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14212 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9667 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 38, 'TRANS': 1169} Chain: "B" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4007 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 482} Chain breaks: 2 Chain: "M" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pyr': 9} Link IDs: {'rna3p': 8} Chain: "N" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'GTA': 1} Classifications: {'RNAv2': 3, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2, None: 1} Not linked: pdbres="GTA N 1 " pdbres=" G N 2 " Chain: "T" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 242 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 10} Link IDs: {'rna3p': 10} Time building chain proxies: 2.95, per 1000 atoms: 0.21 Number of scatterers: 14212 At special positions: 0 Unit cell: (105.138, 144.432, 87.084, 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 54 16.00 P 26 15.00 O 2755 8.00 N 2428 7.00 C 8949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 517.1 milliseconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 16 sheets defined 51.6% alpha, 7.7% beta 6 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.707A pdb=" N GLU A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 36 removed outlier: 3.538A pdb=" N PHE A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.993A pdb=" N ARG A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS A 41 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.734A pdb=" N THR A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 146 through 161 removed outlier: 3.593A pdb=" N CYS A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 removed outlier: 4.032A pdb=" N THR A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.596A pdb=" N ALA A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.706A pdb=" N ILE A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.651A pdb=" N GLY A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 removed outlier: 4.441A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 324 through 340 removed outlier: 3.608A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 removed outlier: 5.054A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.586A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.974A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 431 through 438 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 457 through 460 removed outlier: 3.680A pdb=" N TYR A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.119A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.545A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.653A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.789A pdb=" N VAL A 555 " --> pdb=" O MET A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 574 removed outlier: 4.013A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 645 through 666 Processing helix chain 'A' and resid 689 through 707 removed outlier: 3.540A pdb=" N SER A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 739 removed outlier: 3.783A pdb=" N ILE A 739 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 767 Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.727A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 Processing helix chain 'A' and resid 833 through 839 removed outlier: 3.555A pdb=" N PHE A 838 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET A 839 " --> pdb=" O TRP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 879 removed outlier: 4.134A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 888 removed outlier: 4.247A pdb=" N GLN A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 900 Processing helix chain 'A' and resid 901 through 912 removed outlier: 3.792A pdb=" N ALA A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 923 removed outlier: 3.722A pdb=" N LEU A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 938 removed outlier: 3.600A pdb=" N VAL A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 944 through 959 Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 989 through 1006 removed outlier: 3.689A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A1004 " --> pdb=" O GLU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1019 removed outlier: 3.982A pdb=" N LEU A1019 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1038 removed outlier: 3.742A pdb=" N LYS A1038 " --> pdb=" O PRO A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'A' and resid 1073 through 1081 Processing helix chain 'A' and resid 1090 through 1101 Processing helix chain 'A' and resid 1103 through 1105 No H-bonds generated for 'chain 'A' and resid 1103 through 1105' Processing helix chain 'A' and resid 1106 through 1114 removed outlier: 3.764A pdb=" N VAL A1112 " --> pdb=" O ASN A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1133 Processing helix chain 'A' and resid 1154 through 1162 removed outlier: 3.537A pdb=" N SER A1157 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A1158 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG A1160 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1161 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A1162 " --> pdb=" O GLU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.558A pdb=" N TYR A1168 " --> pdb=" O PRO A1165 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR A1169 " --> pdb=" O PRO A1166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1173 through 1189 removed outlier: 3.714A pdb=" N LEU A1177 " --> pdb=" O GLN A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1212 Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.880A pdb=" N TYR B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 removed outlier: 3.588A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.761A pdb=" N SER B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.554A pdb=" N GLN B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 4.166A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 201 Processing helix chain 'B' and resid 235 through 244 removed outlier: 3.556A pdb=" N GLY B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.604A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 341 removed outlier: 3.693A pdb=" N LEU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.878A pdb=" N PHE B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 4.067A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 441 through 457 removed outlier: 3.599A pdb=" N MET B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 491 through 497 removed outlier: 3.880A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.854A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.511A pdb=" N LYS A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 272 removed outlier: 3.520A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.480A pdb=" N MET A 373 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN A 383 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A 371 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 477 Processing sheet with id=AA6, first strand: chain 'A' and resid 672 through 675 removed outlier: 6.999A pdb=" N ILE A 685 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 623 Processing sheet with id=AA9, first strand: chain 'A' and resid 719 through 721 removed outlier: 3.939A pdb=" N LEU A 726 " --> pdb=" O TRP A 733 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 794 through 796 Processing sheet with id=AB2, first strand: chain 'A' and resid 867 through 868 Processing sheet with id=AB3, first strand: chain 'A' and resid 1023 through 1030 removed outlier: 7.132A pdb=" N GLU A1025 " --> pdb=" O VAL A1201 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A1201 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU A1027 " --> pdb=" O GLY A1199 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY A1199 " --> pdb=" O GLU A1027 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL A1029 " --> pdb=" O ARG A1197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.869A pdb=" N ILE B 158 " --> pdb=" O ILE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 204 through 208 removed outlier: 6.316A pdb=" N ARG B 204 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE B 229 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE B 206 " --> pdb=" O PHE B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 297 through 298 removed outlier: 6.802A pdb=" N GLY B 255 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 257 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 316 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR B 259 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 378 through 381 removed outlier: 6.684A pdb=" N ALA B 347 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL B 487 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B 349 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLY B 489 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 351 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR B 504 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL B 545 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU B 506 " --> pdb=" O VAL B 545 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2264 1.31 - 1.43: 4093 1.43 - 1.56: 8062 1.56 - 1.68: 52 1.68 - 1.81: 96 Bond restraints: 14567 Sorted by residual: bond pdb=" C1B GTA N 1 " pdb=" C2B GTA N 1 " ideal model delta sigma weight residual 1.530 1.303 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1B GTA N 1 " pdb=" O4B GTA N 1 " ideal model delta sigma weight residual 1.395 1.617 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3A GTA N 1 " pdb=" C4A GTA N 1 " ideal model delta sigma weight residual 1.525 1.341 0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" C4A GTA N 1 " pdb=" O4A GTA N 1 " ideal model delta sigma weight residual 1.433 1.607 -0.174 2.00e-02 2.50e+03 7.55e+01 bond pdb=" C4 GTA N 1 " pdb=" N3 GTA N 1 " ideal model delta sigma weight residual 1.330 1.489 -0.159 2.00e-02 2.50e+03 6.31e+01 ... (remaining 14562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 19737 4.37 - 8.75: 90 8.75 - 13.12: 10 13.12 - 17.50: 3 17.50 - 21.87: 3 Bond angle restraints: 19843 Sorted by residual: angle pdb=" N1C GTA N 1 " pdb=" C6C GTA N 1 " pdb=" N6C GTA N 1 " ideal model delta sigma weight residual 119.40 97.53 21.87 3.00e+00 1.11e-01 5.32e+01 angle pdb=" C5C GTA N 1 " pdb=" C6C GTA N 1 " pdb=" N6C GTA N 1 " ideal model delta sigma weight residual 122.62 142.17 -19.55 3.00e+00 1.11e-01 4.25e+01 angle pdb=" O13 GTA N 1 " pdb=" P2 GTA N 1 " pdb=" O23 GTA N 1 " ideal model delta sigma weight residual 93.83 111.45 -17.62 3.00e+00 1.11e-01 3.45e+01 angle pdb=" C1B GTA N 1 " pdb=" N9C GTA N 1 " pdb=" C8C GTA N 1 " ideal model delta sigma weight residual 127.31 110.87 16.44 3.00e+00 1.11e-01 3.00e+01 angle pdb=" C ASP A 749 " pdb=" N ILE A 750 " pdb=" CA ILE A 750 " ideal model delta sigma weight residual 120.69 128.03 -7.34 1.46e+00 4.69e-01 2.53e+01 ... (remaining 19838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.91: 8475 25.91 - 51.82: 203 51.82 - 77.73: 28 77.73 - 103.64: 0 103.64 - 129.55: 1 Dihedral angle restraints: 8707 sinusoidal: 3675 harmonic: 5032 Sorted by residual: dihedral pdb=" C4' A T 11 " pdb=" C3' A T 11 " pdb=" C2' A T 11 " pdb=" C1' A T 11 " ideal model delta sinusoidal sigma weight residual 36.34 -34.70 71.05 1 3.10e+00 1.04e-01 6.75e+02 dihedral pdb=" O4' A T 11 " pdb=" C4' A T 11 " pdb=" C3' A T 11 " pdb=" C2' A T 11 " ideal model delta sinusoidal sigma weight residual -35.15 25.32 -60.47 1 4.00e+00 6.25e-02 3.04e+02 dihedral pdb=" O4' A T 11 " pdb=" C2' A T 11 " pdb=" C1' A T 11 " pdb=" C3' A T 11 " ideal model delta sinusoidal sigma weight residual 25.59 -32.94 58.53 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 8704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1747 0.064 - 0.127: 400 0.127 - 0.191: 53 0.191 - 0.255: 30 0.255 - 0.318: 5 Chirality restraints: 2235 Sorted by residual: chirality pdb=" C3A GTA N 1 " pdb=" C2A GTA N 1 " pdb=" C4A GTA N 1 " pdb=" O3A GTA N 1 " both_signs ideal model delta sigma weight residual False -2.72 -2.40 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB ILE A 881 " pdb=" CA ILE A 881 " pdb=" CG1 ILE A 881 " pdb=" CG2 ILE A 881 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' A T 11 " pdb=" C3' A T 11 " pdb=" O2' A T 11 " pdb=" C1' A T 11 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2232 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " -0.028 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP A 606 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 203 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO A 204 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1014 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A1015 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A1015 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1015 " -0.036 5.00e-02 4.00e+02 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1488 2.75 - 3.28: 13390 3.28 - 3.82: 23455 3.82 - 4.36: 28505 4.36 - 4.90: 48798 Nonbonded interactions: 115636 Sorted by model distance: nonbonded pdb=" OD2 ASP A 766 " pdb=" O2' U M 6 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP A1075 " pdb=" OH TYR A1130 " model vdw 2.282 3.040 nonbonded pdb=" O LYS A 778 " pdb=" OH TYR A 845 " model vdw 2.288 3.040 nonbonded pdb=" OE2 GLU A 947 " pdb=" OH TYR B 135 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR B 352 " pdb=" OD1 ASP B 495 " model vdw 2.308 3.040 ... (remaining 115631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.340 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.490 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.227 14568 Z= 0.348 Angle : 0.982 21.873 19843 Z= 0.489 Chirality : 0.060 0.318 2235 Planarity : 0.006 0.069 2442 Dihedral : 11.261 129.549 5473 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.47 % Allowed : 4.10 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.15), residues: 1701 helix: -2.75 (0.12), residues: 821 sheet: -2.30 (0.36), residues: 149 loop : -2.30 (0.19), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 336 TYR 0.035 0.003 TYR A 331 PHE 0.028 0.003 PHE A 234 TRP 0.064 0.004 TRP A 606 HIS 0.018 0.002 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.35 (14567) covalent geometry : angle 0.98151 / 0.49 (19843) hydrogen bonds : bond 0.16416 / 10.59 ( 562) hydrogen bonds : angle 7.36247 / 5.14 ( 1608) Misc. bond : bond 0.00902 / 0.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 386 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 430 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6889 (mp) REVERT: A 478 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 483 ASP cc_start: 0.7554 (t0) cc_final: 0.6839 (t0) REVERT: A 528 ASP cc_start: 0.7508 (m-30) cc_final: 0.7208 (m-30) REVERT: A 884 MET cc_start: 0.8469 (mtt) cc_final: 0.8176 (mtt) REVERT: A 899 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6548 (mm-30) REVERT: A 906 LEU cc_start: 0.9037 (mt) cc_final: 0.8630 (mp) REVERT: A 955 ASP cc_start: 0.7155 (t0) cc_final: 0.6657 (t0) REVERT: A 1080 ARG cc_start: 0.7475 (ttt180) cc_final: 0.7147 (ttt-90) REVERT: A 1173 GLN cc_start: 0.8333 (pt0) cc_final: 0.8111 (pt0) REVERT: A 1207 ILE cc_start: 0.9122 (mm) cc_final: 0.8875 (mm) REVERT: B 400 SER cc_start: 0.9111 (t) cc_final: 0.8843 (p) REVERT: B 427 ILE cc_start: 0.8789 (mm) cc_final: 0.8509 (mt) REVERT: B 453 ASN cc_start: 0.8866 (m-40) cc_final: 0.8637 (m-40) outliers start: 7 outliers final: 0 residues processed: 390 average time/residue: 0.1367 time to fit residues: 74.7473 Evaluate side-chains 230 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN A 274 GLN A 312 ASN A 412 HIS A 413 HIS A 447 ASN A 522 GLN A 607 GLN A 653 GLN A 696 HIS A 887 GLN A 888 ASN A 939 GLN A 965 ASN A1020 HIS A1108 ASN A1121 GLN B 182 HIS B 393 ASN B 511 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.103001 restraints weight = 20694.628| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.63 r_work: 0.2914 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14568 Z= 0.134 Angle : 0.576 7.710 19843 Z= 0.292 Chirality : 0.043 0.174 2235 Planarity : 0.005 0.054 2442 Dihedral : 8.249 105.792 2224 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.55 % Allowed : 9.14 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.18), residues: 1701 helix: -0.95 (0.16), residues: 832 sheet: -1.90 (0.37), residues: 153 loop : -1.66 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 252 TYR 0.018 0.001 TYR A 969 PHE 0.012 0.001 PHE A 857 TRP 0.030 0.002 TRP A 606 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14567) covalent geometry : angle 0.57594 / 0.29 (19843) hydrogen bonds : bond 0.04163 / 2.71 ( 562) hydrogen bonds : angle 4.80456 / 3.29 ( 1608) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 0.518 Fit side-chains REVERT: A 37 ARG cc_start: 0.8851 (ptt-90) cc_final: 0.8633 (ptt90) REVERT: A 101 TYR cc_start: 0.8768 (m-80) cc_final: 0.8472 (m-80) REVERT: A 104 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8645 (tm) REVERT: A 114 ASN cc_start: 0.7632 (t0) cc_final: 0.7019 (p0) REVERT: A 249 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8866 (pp) REVERT: A 341 ASP cc_start: 0.8507 (t70) cc_final: 0.8174 (t0) REVERT: A 374 SER cc_start: 0.8970 (t) cc_final: 0.8741 (m) REVERT: A 483 ASP cc_start: 0.7877 (t0) cc_final: 0.6952 (t0) REVERT: A 528 ASP cc_start: 0.8451 (m-30) cc_final: 0.8173 (m-30) REVERT: A 623 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7730 (tm-30) REVERT: A 760 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9043 (tp) REVERT: A 768 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8357 (tt) REVERT: A 899 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7268 (mm-30) REVERT: A 959 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7423 (ttp-110) REVERT: A 1023 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 1080 ARG cc_start: 0.7501 (ttt180) cc_final: 0.7048 (ttt-90) REVERT: A 1089 ASP cc_start: 0.7947 (t0) cc_final: 0.7688 (p0) REVERT: A 1207 ILE cc_start: 0.9212 (mm) cc_final: 0.8978 (mm) REVERT: B 400 SER cc_start: 0.9246 (t) cc_final: 0.8906 (p) REVERT: B 427 ILE cc_start: 0.8865 (mm) cc_final: 0.8610 (mt) REVERT: B 447 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8645 (tttt) outliers start: 23 outliers final: 10 residues processed: 267 average time/residue: 0.1409 time to fit residues: 53.5076 Evaluate side-chains 227 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 428 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 108 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 129 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 GLN A 617 GLN A1173 GLN B 429 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.097995 restraints weight = 21024.876| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.56 r_work: 0.2884 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14568 Z= 0.145 Angle : 0.559 8.669 19843 Z= 0.279 Chirality : 0.043 0.192 2235 Planarity : 0.004 0.045 2442 Dihedral : 7.497 111.683 2222 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.96 % Allowed : 10.08 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.19), residues: 1701 helix: -0.01 (0.18), residues: 838 sheet: -1.58 (0.35), residues: 164 loop : -1.46 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 204 TYR 0.016 0.001 TYR A 969 PHE 0.012 0.001 PHE A 206 TRP 0.022 0.002 TRP A 606 HIS 0.004 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14567) covalent geometry : angle 0.55875 / 0.28 (19843) hydrogen bonds : bond 0.03863 / 2.53 ( 562) hydrogen bonds : angle 4.46686 / 3.05 ( 1608) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.583 Fit side-chains REVERT: A 101 TYR cc_start: 0.8616 (m-80) cc_final: 0.8382 (m-80) REVERT: A 114 ASN cc_start: 0.7642 (t0) cc_final: 0.7004 (p0) REVERT: A 249 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8863 (pp) REVERT: A 382 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8873 (mtpp) REVERT: A 483 ASP cc_start: 0.7867 (t0) cc_final: 0.6965 (t0) REVERT: A 528 ASP cc_start: 0.8518 (m-30) cc_final: 0.8199 (m-30) REVERT: A 623 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 678 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8948 (tt) REVERT: A 760 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9031 (tp) REVERT: A 768 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 899 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 955 ASP cc_start: 0.8075 (m-30) cc_final: 0.7826 (m-30) REVERT: A 1080 ARG cc_start: 0.7748 (ttt180) cc_final: 0.7303 (ttt-90) REVERT: A 1089 ASP cc_start: 0.8003 (t0) cc_final: 0.7756 (p0) REVERT: A 1207 ILE cc_start: 0.9199 (mm) cc_final: 0.8986 (mm) REVERT: B 212 ASN cc_start: 0.8389 (t0) cc_final: 0.7907 (t0) REVERT: B 400 SER cc_start: 0.9234 (t) cc_final: 0.8904 (p) REVERT: B 427 ILE cc_start: 0.8856 (mm) cc_final: 0.8617 (mt) outliers start: 44 outliers final: 24 residues processed: 263 average time/residue: 0.1386 time to fit residues: 52.4441 Evaluate side-chains 238 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 42 optimal weight: 30.0000 chunk 167 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 145 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.099180 restraints weight = 20887.550| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.56 r_work: 0.2865 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14568 Z= 0.146 Angle : 0.547 9.319 19843 Z= 0.272 Chirality : 0.043 0.208 2235 Planarity : 0.004 0.041 2442 Dihedral : 7.359 111.752 2222 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.23 % Allowed : 10.28 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.20), residues: 1701 helix: 0.37 (0.18), residues: 844 sheet: -1.48 (0.35), residues: 166 loop : -1.29 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 744 TYR 0.017 0.001 TYR A 969 PHE 0.012 0.001 PHE A 206 TRP 0.018 0.001 TRP A 606 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (14567) covalent geometry : angle 0.54682 / 0.27 (19843) hydrogen bonds : bond 0.03713 / 2.44 ( 562) hydrogen bonds : angle 4.36385 / 2.98 ( 1608) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.554 Fit side-chains REVERT: A 101 TYR cc_start: 0.8668 (m-80) cc_final: 0.8460 (m-80) REVERT: A 114 ASN cc_start: 0.7626 (t0) cc_final: 0.7014 (p0) REVERT: A 249 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8888 (pp) REVERT: A 382 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8878 (mtpp) REVERT: A 483 ASP cc_start: 0.7794 (t0) cc_final: 0.6864 (t0) REVERT: A 596 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7683 (mp10) REVERT: A 623 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 760 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9022 (tp) REVERT: A 768 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8473 (tp) REVERT: A 805 TYR cc_start: 0.6064 (t80) cc_final: 0.5849 (t80) REVERT: A 899 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 955 ASP cc_start: 0.8127 (m-30) cc_final: 0.7750 (m-30) REVERT: A 1080 ARG cc_start: 0.7805 (ttt180) cc_final: 0.7338 (ttt-90) REVERT: A 1089 ASP cc_start: 0.7986 (t0) cc_final: 0.7718 (p0) REVERT: A 1207 ILE cc_start: 0.9209 (mm) cc_final: 0.8991 (mm) REVERT: B 55 MET cc_start: 0.9033 (tpp) cc_final: 0.8827 (ttt) REVERT: B 204 ARG cc_start: 0.8518 (ttp-110) cc_final: 0.8181 (mtp85) REVERT: B 212 ASN cc_start: 0.8462 (t0) cc_final: 0.7890 (t0) REVERT: B 400 SER cc_start: 0.9238 (t) cc_final: 0.8936 (p) REVERT: B 427 ILE cc_start: 0.8866 (mm) cc_final: 0.8578 (mt) REVERT: B 550 MET cc_start: 0.9320 (mtp) cc_final: 0.9043 (mtm) outliers start: 48 outliers final: 37 residues processed: 251 average time/residue: 0.1311 time to fit residues: 47.7900 Evaluate side-chains 244 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 107 optimal weight: 10.0000 chunk 144 optimal weight: 0.0570 chunk 128 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.115121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.096382 restraints weight = 21077.386| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.57 r_work: 0.2848 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14568 Z= 0.169 Angle : 0.560 10.019 19843 Z= 0.279 Chirality : 0.044 0.227 2235 Planarity : 0.004 0.037 2442 Dihedral : 7.333 113.230 2222 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.83 % Allowed : 10.48 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1701 helix: 0.55 (0.18), residues: 842 sheet: -1.46 (0.35), residues: 168 loop : -1.23 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 744 TYR 0.018 0.001 TYR A 969 PHE 0.013 0.001 PHE A 206 TRP 0.017 0.001 TRP A 606 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (14567) covalent geometry : angle 0.55991 / 0.28 (19843) hydrogen bonds : bond 0.03830 / 2.52 ( 562) hydrogen bonds : angle 4.37668 / 2.99 ( 1608) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 0.534 Fit side-chains REVERT: A 101 TYR cc_start: 0.8664 (m-80) cc_final: 0.8447 (m-80) REVERT: A 114 ASN cc_start: 0.7460 (t0) cc_final: 0.6915 (p0) REVERT: A 249 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8883 (pp) REVERT: A 250 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8093 (ttmm) REVERT: A 377 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8377 (ttt90) REVERT: A 382 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8827 (mtpp) REVERT: A 596 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7723 (mp10) REVERT: A 623 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 760 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9046 (tp) REVERT: A 768 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8547 (tp) REVERT: A 899 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7136 (mm-30) REVERT: A 955 ASP cc_start: 0.8118 (m-30) cc_final: 0.7688 (m-30) REVERT: A 1080 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7340 (ttt-90) REVERT: A 1089 ASP cc_start: 0.8022 (t0) cc_final: 0.7752 (p0) REVERT: B 204 ARG cc_start: 0.8506 (ttp-110) cc_final: 0.8033 (mtp180) REVERT: B 212 ASN cc_start: 0.8505 (t0) cc_final: 0.7847 (t0) REVERT: B 224 MET cc_start: 0.8906 (mpp) cc_final: 0.8572 (mpp) REVERT: B 400 SER cc_start: 0.9265 (t) cc_final: 0.8975 (p) REVERT: B 427 ILE cc_start: 0.8872 (mm) cc_final: 0.8606 (mt) REVERT: B 550 MET cc_start: 0.9378 (mtp) cc_final: 0.9070 (mtm) outliers start: 57 outliers final: 45 residues processed: 248 average time/residue: 0.1343 time to fit residues: 47.8062 Evaluate side-chains 250 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 113 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 160 optimal weight: 0.1980 chunk 162 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.096874 restraints weight = 20937.493| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.56 r_work: 0.2854 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14568 Z= 0.153 Angle : 0.552 10.754 19843 Z= 0.274 Chirality : 0.043 0.233 2235 Planarity : 0.003 0.033 2442 Dihedral : 7.270 113.224 2222 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.83 % Allowed : 11.09 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1701 helix: 0.69 (0.18), residues: 842 sheet: -1.45 (0.35), residues: 168 loop : -1.15 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 744 TYR 0.019 0.001 TYR A 969 PHE 0.011 0.001 PHE A 206 TRP 0.014 0.001 TRP A 606 HIS 0.004 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (14567) covalent geometry : angle 0.55217 / 0.27 (19843) hydrogen bonds : bond 0.03689 / 2.43 ( 562) hydrogen bonds : angle 4.32221 / 2.95 ( 1608) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 206 time to evaluate : 0.544 Fit side-chains REVERT: A 101 TYR cc_start: 0.8641 (m-80) cc_final: 0.8416 (m-80) REVERT: A 114 ASN cc_start: 0.7661 (t0) cc_final: 0.6979 (p0) REVERT: A 249 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8888 (pp) REVERT: A 250 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8139 (ttmm) REVERT: A 377 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8395 (ttt90) REVERT: A 382 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8839 (mtpp) REVERT: A 434 GLU cc_start: 0.8036 (mp0) cc_final: 0.7792 (pm20) REVERT: A 596 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7809 (mp10) REVERT: A 760 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9057 (tp) REVERT: A 768 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8563 (tt) REVERT: A 812 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6072 (pmt) REVERT: A 899 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7151 (mm-30) REVERT: A 955 ASP cc_start: 0.8115 (m-30) cc_final: 0.7642 (m-30) REVERT: A 1080 ARG cc_start: 0.7940 (ttt180) cc_final: 0.7507 (ttt-90) REVERT: A 1089 ASP cc_start: 0.8009 (t0) cc_final: 0.7757 (p0) REVERT: B 204 ARG cc_start: 0.8563 (ttp-110) cc_final: 0.8137 (mtp180) REVERT: B 212 ASN cc_start: 0.8522 (t0) cc_final: 0.7877 (t0) REVERT: B 400 SER cc_start: 0.9251 (t) cc_final: 0.8981 (p) REVERT: B 427 ILE cc_start: 0.8895 (mm) cc_final: 0.8624 (mt) outliers start: 57 outliers final: 43 residues processed: 245 average time/residue: 0.1299 time to fit residues: 46.2843 Evaluate side-chains 246 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.095189 restraints weight = 20993.767| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.57 r_work: 0.2841 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14568 Z= 0.169 Angle : 0.565 11.236 19843 Z= 0.281 Chirality : 0.044 0.244 2235 Planarity : 0.004 0.032 2442 Dihedral : 7.272 115.092 2222 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.83 % Allowed : 11.42 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1701 helix: 0.69 (0.18), residues: 844 sheet: -1.56 (0.35), residues: 168 loop : -1.05 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 744 TYR 0.019 0.001 TYR A 969 PHE 0.012 0.001 PHE A 566 TRP 0.015 0.001 TRP A 445 HIS 0.004 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (14567) covalent geometry : angle 0.56549 / 0.28 (19843) hydrogen bonds : bond 0.03807 / 2.51 ( 562) hydrogen bonds : angle 4.33467 / 2.97 ( 1608) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 0.574 Fit side-chains REVERT: A 114 ASN cc_start: 0.7640 (t0) cc_final: 0.6989 (p0) REVERT: A 249 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8891 (pp) REVERT: A 250 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8194 (ttmm) REVERT: A 377 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8431 (ttt90) REVERT: A 382 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8847 (mtpp) REVERT: A 434 GLU cc_start: 0.8007 (mp0) cc_final: 0.7775 (pm20) REVERT: A 760 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9054 (tp) REVERT: A 768 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8607 (tt) REVERT: A 812 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6090 (pmt) REVERT: A 899 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 955 ASP cc_start: 0.8088 (m-30) cc_final: 0.7595 (m-30) REVERT: A 1080 ARG cc_start: 0.8002 (ttt180) cc_final: 0.7571 (ttt-90) REVERT: A 1089 ASP cc_start: 0.8052 (t0) cc_final: 0.7779 (p0) REVERT: A 1136 ASN cc_start: 0.8063 (p0) cc_final: 0.7851 (p0) REVERT: B 204 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.8133 (mtp180) REVERT: B 212 ASN cc_start: 0.8568 (t0) cc_final: 0.7921 (t0) REVERT: B 400 SER cc_start: 0.9249 (t) cc_final: 0.8970 (p) REVERT: B 427 ILE cc_start: 0.8890 (mm) cc_final: 0.8612 (mt) REVERT: B 550 MET cc_start: 0.9344 (mtp) cc_final: 0.9004 (mtm) outliers start: 57 outliers final: 46 residues processed: 240 average time/residue: 0.1369 time to fit residues: 47.1582 Evaluate side-chains 245 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 78 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 72 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.094377 restraints weight = 21074.497| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.58 r_work: 0.2822 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14568 Z= 0.190 Angle : 0.584 12.171 19843 Z= 0.291 Chirality : 0.045 0.260 2235 Planarity : 0.004 0.032 2442 Dihedral : 7.330 117.978 2222 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.83 % Allowed : 11.83 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1701 helix: 0.65 (0.18), residues: 845 sheet: -1.43 (0.35), residues: 168 loop : -1.17 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 744 TYR 0.021 0.002 TYR A 969 PHE 0.013 0.001 PHE A 206 TRP 0.017 0.002 TRP A 445 HIS 0.005 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (14567) covalent geometry : angle 0.58411 / 0.29 (19843) hydrogen bonds : bond 0.03970 / 2.62 ( 562) hydrogen bonds : angle 4.38012 / 3.00 ( 1608) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 197 time to evaluate : 0.419 Fit side-chains REVERT: A 114 ASN cc_start: 0.7710 (t0) cc_final: 0.7074 (p0) REVERT: A 249 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8933 (pp) REVERT: A 250 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8253 (ttmm) REVERT: A 377 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8435 (ttt90) REVERT: A 382 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8874 (mtpp) REVERT: A 596 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7932 (mp10) REVERT: A 760 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9076 (tp) REVERT: A 768 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 777 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9105 (tp) REVERT: A 812 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6117 (pmt) REVERT: A 899 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7158 (mm-30) REVERT: A 955 ASP cc_start: 0.8068 (m-30) cc_final: 0.7589 (m-30) REVERT: A 1080 ARG cc_start: 0.8059 (ttt180) cc_final: 0.7624 (ttt-90) REVERT: A 1089 ASP cc_start: 0.8171 (t0) cc_final: 0.7838 (p0) REVERT: B 204 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8268 (mtp180) REVERT: B 212 ASN cc_start: 0.8589 (t0) cc_final: 0.7947 (t0) REVERT: B 355 LYS cc_start: 0.8993 (tttm) cc_final: 0.8734 (tttp) REVERT: B 400 SER cc_start: 0.9246 (t) cc_final: 0.8993 (p) REVERT: B 550 MET cc_start: 0.9365 (mtp) cc_final: 0.9071 (mtm) outliers start: 57 outliers final: 47 residues processed: 234 average time/residue: 0.1333 time to fit residues: 44.6690 Evaluate side-chains 246 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 54 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.093947 restraints weight = 21094.977| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.58 r_work: 0.2809 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14568 Z= 0.196 Angle : 0.597 12.990 19843 Z= 0.297 Chirality : 0.045 0.272 2235 Planarity : 0.004 0.032 2442 Dihedral : 7.357 119.960 2222 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.90 % Allowed : 11.83 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1701 helix: 0.65 (0.18), residues: 845 sheet: -1.42 (0.35), residues: 168 loop : -1.16 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 744 TYR 0.022 0.002 TYR A 969 PHE 0.013 0.001 PHE A 566 TRP 0.020 0.002 TRP A 445 HIS 0.005 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (14567) covalent geometry : angle 0.59677 / 0.30 (19843) hydrogen bonds : bond 0.04017 / 2.66 ( 562) hydrogen bonds : angle 4.40344 / 3.02 ( 1608) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 197 time to evaluate : 0.550 Fit side-chains REVERT: A 114 ASN cc_start: 0.7680 (t0) cc_final: 0.7036 (p0) REVERT: A 250 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8285 (ttmm) REVERT: A 377 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8433 (ttt90) REVERT: A 382 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8853 (mtpp) REVERT: A 596 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7931 (mp10) REVERT: A 760 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9050 (tp) REVERT: A 768 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8692 (tt) REVERT: A 777 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9102 (tp) REVERT: A 812 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6120 (pmt) REVERT: A 899 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7173 (mm-30) REVERT: A 911 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6281 (tp) REVERT: A 955 ASP cc_start: 0.8052 (m-30) cc_final: 0.7593 (m-30) REVERT: A 1080 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7641 (ttt-90) REVERT: A 1089 ASP cc_start: 0.8164 (t0) cc_final: 0.7834 (p0) REVERT: B 204 ARG cc_start: 0.8561 (ttp-110) cc_final: 0.8281 (mtp180) REVERT: B 212 ASN cc_start: 0.8589 (t0) cc_final: 0.7946 (t0) REVERT: B 355 LYS cc_start: 0.8998 (tttm) cc_final: 0.8725 (tttp) REVERT: B 400 SER cc_start: 0.9288 (t) cc_final: 0.9014 (p) REVERT: B 550 MET cc_start: 0.9384 (mtp) cc_final: 0.9111 (mtm) outliers start: 58 outliers final: 47 residues processed: 240 average time/residue: 0.1316 time to fit residues: 45.5175 Evaluate side-chains 245 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 91 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 4 optimal weight: 0.2980 chunk 127 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.097984 restraints weight = 20821.988| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.61 r_work: 0.2882 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14568 Z= 0.099 Angle : 0.531 13.829 19843 Z= 0.264 Chirality : 0.042 0.245 2235 Planarity : 0.003 0.031 2442 Dihedral : 7.069 111.635 2222 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.69 % Allowed : 13.44 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1701 helix: 0.98 (0.19), residues: 850 sheet: -1.23 (0.36), residues: 166 loop : -0.97 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 993 TYR 0.021 0.001 TYR A 969 PHE 0.008 0.001 PHE A 206 TRP 0.018 0.001 TRP A 445 HIS 0.003 0.001 HIS A 648 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (14567) covalent geometry : angle 0.53124 / 0.26 (19843) hydrogen bonds : bond 0.03159 / 2.08 ( 562) hydrogen bonds : angle 4.14898 / 2.83 ( 1608) Misc. bond : bond 0.00027 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.559 Fit side-chains REVERT: A 101 TYR cc_start: 0.8613 (m-80) cc_final: 0.8362 (m-10) REVERT: A 114 ASN cc_start: 0.7699 (t0) cc_final: 0.7071 (p0) REVERT: A 377 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8384 (ttt90) REVERT: A 382 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8908 (mtpp) REVERT: A 596 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8003 (mp10) REVERT: A 768 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8592 (tt) REVERT: A 812 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.5943 (pmt) REVERT: A 899 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7160 (mm-30) REVERT: A 911 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6233 (tp) REVERT: A 955 ASP cc_start: 0.8115 (m-30) cc_final: 0.7640 (m-30) REVERT: A 1080 ARG cc_start: 0.8022 (ttt180) cc_final: 0.7556 (ttt-90) REVERT: A 1089 ASP cc_start: 0.8124 (t0) cc_final: 0.7778 (p0) REVERT: B 78 THR cc_start: 0.9076 (m) cc_final: 0.8762 (p) REVERT: B 204 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8220 (mtp180) REVERT: B 212 ASN cc_start: 0.8514 (t0) cc_final: 0.7927 (t0) REVERT: B 224 MET cc_start: 0.8877 (mpp) cc_final: 0.8546 (mpp) REVERT: B 400 SER cc_start: 0.9295 (t) cc_final: 0.9049 (p) REVERT: B 427 ILE cc_start: 0.8909 (mm) cc_final: 0.8619 (mt) REVERT: B 550 MET cc_start: 0.9268 (mtp) cc_final: 0.9010 (mtm) outliers start: 40 outliers final: 26 residues processed: 253 average time/residue: 0.1285 time to fit residues: 46.7579 Evaluate side-chains 237 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 66 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 81 optimal weight: 0.0870 chunk 144 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 overall best weight: 3.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.096329 restraints weight = 20927.710| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.58 r_work: 0.2852 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14568 Z= 0.136 Angle : 0.556 13.051 19843 Z= 0.276 Chirality : 0.043 0.249 2235 Planarity : 0.003 0.031 2442 Dihedral : 7.080 111.731 2222 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.42 % Allowed : 14.05 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1701 helix: 1.01 (0.19), residues: 843 sheet: -1.25 (0.35), residues: 168 loop : -0.93 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 252 TYR 0.021 0.001 TYR A 969 PHE 0.010 0.001 PHE A 566 TRP 0.019 0.001 TRP A 445 HIS 0.004 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14567) covalent geometry : angle 0.55558 / 0.28 (19843) hydrogen bonds : bond 0.03453 / 2.28 ( 562) hydrogen bonds : angle 4.17649 / 2.84 ( 1608) Misc. bond : bond 0.00034 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2982.71 seconds wall clock time: 52 minutes 4.67 seconds (3124.67 seconds total)