Starting phenix.real_space_refine on Thu Aug 6 22:07:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8foj_29351/08_2026/8foj_29351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foj_29351/08_2026/8foj_29351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8foj_29351/08_2026/8foj_29351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foj_29351/08_2026/8foj_29351.map" model { file = "/net/cci-nas-00/data/ceres_data/8foj_29351/08_2026/8foj_29351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foj_29351/08_2026/8foj_29351.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8foj_29351/08_2026/8foj_29351.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8foj_29351/08_2026/8foj_29351.cif" } resolution = 4.8 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 21 5.49 5 S 95 5.16 5 C 11100 2.51 5 N 2971 2.21 5 O 3347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17538 Number of models: 1 Model: "" Number of chains: 7 Chain: "1" Number of atoms: 7536 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 961, 7528 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 44, 'TRANS': 916} Chain breaks: 13 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 14, 'TYR:plan': 2, 'GLN:plan1': 4, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 128 Conformer: "B" Number of residues, atoms: 961, 7528 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 44, 'TRANS': 916} Chain breaks: 13 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 14, 'TYR:plan': 2, 'GLN:plan1': 4, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 128 bond proxies already assigned to first conformer: 7649 Chain: "A" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2713 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 316} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 3532 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 428, 3509 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 428, 3509 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 3559 Chain: "C" Number of atoms: 3308 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3294 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 426, 3294 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 3355 Chain: "T" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 220 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12474 SG CYS B 336 80.144 94.688 100.636 1.00158.95 S ATOM 13241 SG CYS B 434 85.313 90.717 99.433 1.00138.98 S ATOM 13113 SG CYS B 417 81.693 88.069 98.997 1.00123.59 S ATOM 13559 SG CYS B 474 82.138 90.534 104.905 1.00120.32 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS C 399 " occ=0.34 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.66 Time building chain proxies: 6.14, per 1000 atoms: 0.35 Number of scatterers: 17538 At special positions: 0 Unit cell: (133.308, 148.212, 187.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 95 16.00 P 21 15.00 O 3347 8.00 N 2971 7.00 C 11100 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=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " Number of angles added : 12 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4146 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 19 sheets defined 51.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain '1' and resid 402 through 419 Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 480 through 489 Processing helix chain '1' and resid 521 through 523 No H-bonds generated for 'chain '1' and resid 521 through 523' Processing helix chain '1' and resid 615 through 631 removed outlier: 3.734A pdb=" N MET 1 619 " --> pdb=" O ASN 1 615 " (cutoff:3.500A) Processing helix chain '1' and resid 643 through 655 Processing helix chain '1' and resid 659 through 664 removed outlier: 3.571A pdb=" N ILE 1 663 " --> pdb=" O PHE 1 660 " (cutoff:3.500A) Processing helix chain '1' and resid 682 through 691 Processing helix chain '1' and resid 701 through 707 removed outlier: 3.540A pdb=" N LEU 1 707 " --> pdb=" O MET 1 703 " (cutoff:3.500A) Processing helix chain '1' and resid 715 through 725 Processing helix chain '1' and resid 737 through 742 removed outlier: 3.666A pdb=" N ASN 1 742 " --> pdb=" O GLN 1 739 " (cutoff:3.500A) Processing helix chain '1' and resid 743 through 769 removed outlier: 3.629A pdb=" N MET 1 747 " --> pdb=" O ASP 1 743 " (cutoff:3.500A) Processing helix chain '1' and resid 769 through 782 Processing helix chain '1' and resid 784 through 791 Processing helix chain '1' and resid 798 through 807 Processing helix chain '1' and resid 867 through 877 Processing helix chain '1' and resid 904 through 927 removed outlier: 3.679A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 929 through 949 Processing helix chain '1' and resid 950 through 954 Processing helix chain '1' and resid 963 through 988 Processing helix chain '1' and resid 1008 through 1027 Processing helix chain '1' and resid 1071 through 1075 Processing helix chain '1' and resid 1079 through 1093 Processing helix chain '1' and resid 1101 through 1120 Processing helix chain '1' and resid 1123 through 1128 Processing helix chain '1' and resid 1146 through 1159 Processing helix chain '1' and resid 1196 through 1201 removed outlier: 3.619A pdb=" N ILE 11201 " --> pdb=" O ASN 11197 " (cutoff:3.500A) Processing helix chain '1' and resid 1202 through 1205 removed outlier: 3.687A pdb=" N ASN 11205 " --> pdb=" O LYS 11202 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1202 through 1205' Processing helix chain '1' and resid 1209 through 1217 Processing helix chain '1' and resid 1218 through 1226 Processing helix chain '1' and resid 1233 through 1240 Processing helix chain '1' and resid 1322 through 1343 removed outlier: 4.547A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1381 through 1396 Processing helix chain '1' and resid 1397 through 1404 Processing helix chain '1' and resid 1423 through 1434 Processing helix chain '1' and resid 1434 through 1450 removed outlier: 4.199A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 34 removed outlier: 3.684A pdb=" N HIS A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.698A pdb=" N ASP A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 151 removed outlier: 4.774A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.512A pdb=" N ALA A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 210 through 229 Proline residue: A 222 - end of helix removed outlier: 3.911A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.778A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 removed outlier: 3.750A pdb=" N HIS A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.079A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 320' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 372 through 393 Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 71 through 95 removed outlier: 3.527A pdb=" N ARG B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 120 through 139 removed outlier: 3.677A pdb=" N CYS B 139 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 191 through 207 removed outlier: 3.668A pdb=" N LEU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.605A pdb=" N ARG B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.759A pdb=" N ASN B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 282 Proline residue: B 279 - end of helix Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 322 through 325 removed outlier: 3.553A pdb=" N TRP B 325 " --> pdb=" O GLN B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 322 through 325' Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 334 through 348 Processing helix chain 'B' and resid 351 through 366 Processing helix chain 'B' and resid 368 through 380 removed outlier: 3.746A pdb=" N PHE B 380 " --> pdb=" O TRP B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.512A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 482 removed outlier: 3.657A pdb=" N ALA B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 removed outlier: 3.614A pdb=" N GLN B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 276 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.528A pdb=" N GLY C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 460 through 474 removed outlier: 3.852A pdb=" N THR C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Proline residue: C 471 - end of helix Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 548 through 554 removed outlier: 3.700A pdb=" N SER C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 613 through 621 removed outlier: 5.210A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 Processing helix chain 'C' and resid 693 through 697 removed outlier: 3.684A pdb=" N ARG C 697 " --> pdb=" O ASN C 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 693 through 697' Processing sheet with id=AA1, first strand: chain '1' and resid 515 through 519 removed outlier: 6.689A pdb=" N SER 1 381 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL 1 517 " --> pdb=" O SER 1 381 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET 1 383 " --> pdb=" O VAL 1 517 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL 1 519 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 519 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET 1 354 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 424 through 431 removed outlier: 4.623A pdb=" N ARG 1 424 " --> pdb=" O LEU 1 449 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET 1 430 " --> pdb=" O SER 1 443 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER 1 443 " --> pdb=" O MET 1 430 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU 1 446 " --> pdb=" O PHE 1 395 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE 1 395 " --> pdb=" O LEU 1 446 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE 1 394 " --> pdb=" O VAL 1 474 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL 1 474 " --> pdb=" O PHE 1 394 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU 1 396 " --> pdb=" O TYR 1 472 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 610 through 612 removed outlier: 7.817A pdb=" N ARG 1 611 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR 1 584 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS 1 553 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN 1 544 " --> pdb=" O VAL 1 557 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE 1 559 " --> pdb=" O SER 1 542 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER 1 542 " --> pdb=" O ILE 1 559 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU 1 561 " --> pdb=" O SER 1 540 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER 1 540 " --> pdb=" O LEU 1 561 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA 1 563 " --> pdb=" O CYS 1 538 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS 1 538 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU 1 539 " --> pdb=" O ILE 1 636 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 854 through 856 removed outlier: 3.968A pdb=" N LEU 11041 " --> pdb=" O HIS 1 856 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP 11033 " --> pdb=" O ASP 1 864 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL 1 862 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL 11037 " --> pdb=" O VAL 1 860 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL 1 860 " --> pdb=" O VAL 11037 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR 1 994 " --> pdb=" O MET 11001 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP 11003 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL 1 992 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 854 through 856 removed outlier: 3.968A pdb=" N LEU 11041 " --> pdb=" O HIS 1 856 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE 11038 " --> pdb=" O VAL 11054 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL 11054 " --> pdb=" O PHE 11038 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS 11040 " --> pdb=" O LEU 11052 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 1129 through 1132 removed outlier: 3.694A pdb=" N ILE 11168 " --> pdb=" O MET 11131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 1284 through 1286 Processing sheet with id=AA8, first strand: chain '1' and resid 1305 through 1307 Processing sheet with id=AA9, first strand: chain '1' and resid 1356 through 1357 Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 48 removed outlier: 4.578A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 48 removed outlier: 4.578A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 325 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 108 through 112 removed outlier: 4.457A pdb=" N TRP A 159 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 181 through 182 removed outlier: 4.091A pdb=" N GLN B 181 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 302 removed outlier: 5.033A pdb=" N LEU C 316 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG C 331 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 362 " --> pdb=" O ARG C 331 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP C 333 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N SER C 364 " --> pdb=" O ASP C 333 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 349 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 298 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 352 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 376 removed outlier: 4.267A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 515 through 517 removed outlier: 3.643A pdb=" N MET C 431 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 522 through 526 Processing sheet with id=AC1, first strand: chain 'C' and resid 578 through 579 removed outlier: 3.858A pdb=" N SER C 608 " --> pdb=" O ARG C 579 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.11: 1 1.11 - 1.41: 7290 1.41 - 1.70: 10516 1.70 - 1.99: 132 1.99 - 2.29: 13 Bond restraints: 17952 Sorted by residual: bond pdb=" CG PRO C 471 " pdb=" CD PRO C 471 " ideal model delta sigma weight residual 1.503 0.821 0.682 3.40e-02 8.65e+02 4.02e+02 bond pdb=" CB PRO C 471 " pdb=" CG PRO C 471 " ideal model delta sigma weight residual 1.492 2.276 -0.784 5.00e-02 4.00e+02 2.46e+02 bond pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " ideal model delta sigma weight residual 1.533 1.421 0.113 1.42e-02 4.96e+03 6.28e+01 bond pdb=" N PRO C 471 " pdb=" CA PRO C 471 " ideal model delta sigma weight residual 1.469 1.554 -0.085 1.28e-02 6.10e+03 4.45e+01 bond pdb=" CA THR C 306 " pdb=" CB THR C 306 " ideal model delta sigma weight residual 1.525 1.582 -0.057 1.47e-02 4.63e+03 1.50e+01 ... (remaining 17947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.57: 24406 10.57 - 21.13: 5 21.13 - 31.70: 0 31.70 - 42.27: 1 42.27 - 52.84: 2 Bond angle restraints: 24414 Sorted by residual: angle pdb=" N PRO C 471 " pdb=" CD PRO C 471 " pdb=" CG PRO C 471 " ideal model delta sigma weight residual 103.20 51.14 52.06 1.50e+00 4.44e-01 1.20e+03 angle pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " pdb=" CG PRO C 471 " ideal model delta sigma weight residual 104.50 51.66 52.84 1.90e+00 2.77e-01 7.73e+02 angle pdb=" N PRO C 471 " pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " ideal model delta sigma weight residual 103.25 86.06 17.19 1.05e+00 9.07e-01 2.68e+02 angle pdb=" CA PRO C 471 " pdb=" N PRO C 471 " pdb=" CD PRO C 471 " ideal model delta sigma weight residual 112.00 92.13 19.87 1.40e+00 5.10e-01 2.02e+02 angle pdb=" CB PRO C 471 " pdb=" CG PRO C 471 " pdb=" CD PRO C 471 " ideal model delta sigma weight residual 106.10 68.87 37.23 3.20e+00 9.77e-02 1.35e+02 ... (remaining 24409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.14: 10512 28.14 - 56.28: 294 56.28 - 84.42: 30 84.42 - 112.57: 8 112.57 - 140.71: 1 Dihedral angle restraints: 10845 sinusoidal: 4474 harmonic: 6371 Sorted by residual: dihedral pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " pdb=" CG PRO C 471 " pdb=" CD PRO C 471 " ideal model delta sinusoidal sigma weight residual -38.00 -178.71 140.71 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" N PRO C 471 " pdb=" C PRO C 471 " pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " ideal model delta harmonic sigma weight residual 115.10 99.06 16.04 0 2.50e+00 1.60e-01 4.12e+01 dihedral pdb=" CA PHE C 350 " pdb=" C PHE C 350 " pdb=" N LYS C 351 " pdb=" CA LYS C 351 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 10842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2281 0.056 - 0.111: 422 0.111 - 0.167: 34 0.167 - 0.223: 2 0.223 - 0.278: 11 Chirality restraints: 2750 Sorted by residual: chirality pdb=" CB ILE C 633 " pdb=" CA ILE C 633 " pdb=" CG1 ILE C 633 " pdb=" CG2 ILE C 633 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" P G P 3 " pdb=" OP1 G P 3 " pdb=" OP2 G P 3 " pdb=" O5' G P 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" P G P 7 " pdb=" OP1 G P 7 " pdb=" OP2 G P 7 " pdb=" O5' G P 7 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2747 not shown) Planarity restraints: 3071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 470 " -0.090 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO C 471 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO C 471 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 471 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP 1 671 " -0.081 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO 1 672 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO 1 672 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO 1 672 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 1 929 " 0.066 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO 1 930 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO 1 930 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO 1 930 " 0.053 5.00e-02 4.00e+02 ... (remaining 3068 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 359 2.69 - 3.24: 17511 3.24 - 3.79: 27490 3.79 - 4.35: 36395 4.35 - 4.90: 58396 Nonbonded interactions: 140151 Sorted by model distance: nonbonded pdb=" O VAL A 191 " pdb=" OH TYR A 310 " model vdw 2.138 3.040 nonbonded pdb=" C THR C 470 " pdb=" CG PRO C 471 " model vdw 2.149 2.936 nonbonded pdb=" O CYS 1 953 " pdb=" OG SER 1 959 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR A 122 " pdb=" O GLN A 232 " model vdw 2.208 3.040 nonbonded pdb=" OG SER 1 433 " pdb=" O PHE 1 880 " model vdw 2.221 3.040 ... (remaining 140146 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.210 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.340 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 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 : 0.009 0.784 17956 Z= 0.278 Angle : 0.995 52.835 24426 Z= 0.533 Chirality : 0.045 0.278 2750 Planarity : 0.006 0.121 3071 Dihedral : 13.339 140.708 6699 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.05 % Allowed : 0.27 % Favored : 99.68 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.71 % 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: 0.08 (0.18), residues: 2109 helix: 0.67 (0.17), residues: 969 sheet: -0.47 (0.32), residues: 244 loop : -0.34 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 121 TYR 0.018 0.002 TYR C 295 PHE 0.026 0.002 PHE B 75 TRP 0.065 0.003 TRP 1 785 HIS 0.009 0.001 HIS 11316 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.28 (17952) covalent geometry : angle 0.90985 / 0.53 (24414) hydrogen bonds : bond 0.17054 / 11.02 ( 850) hydrogen bonds : angle 6.93115 / 4.97 ( 2413) metal coordination : bond 0.00862 / 0.44 ( 4) metal coordination : angle 18.18851 / 10.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6253 (mtp) cc_final: 0.5872 (mtp) REVERT: 1 430 MET cc_start: 0.8137 (mtt) cc_final: 0.7656 (mtp) REVERT: 1 445 TYR cc_start: 0.4440 (m-80) cc_final: 0.3991 (m-80) REVERT: 1 619 MET cc_start: 0.6365 (ttt) cc_final: 0.6047 (ttt) REVERT: 1 929 ASP cc_start: 0.8501 (m-30) cc_final: 0.8289 (m-30) REVERT: 1 1237 LEU cc_start: 0.4920 (tp) cc_final: 0.4277 (tp) REVERT: 1 1341 TYR cc_start: 0.7363 (t80) cc_final: 0.6559 (t80) REVERT: 1 1351 SER cc_start: 0.9179 (m) cc_final: 0.8893 (t) REVERT: 1 1376 MET cc_start: 0.7845 (tpp) cc_final: 0.7488 (tpp) REVERT: 1 1392 PHE cc_start: 0.7055 (m-10) cc_final: 0.6852 (m-10) REVERT: 1 1404 GLN cc_start: 0.6865 (mt0) cc_final: 0.6454 (mt0) REVERT: A 141 MET cc_start: 0.5944 (mtm) cc_final: 0.5624 (mtm) REVERT: A 158 ILE cc_start: 0.7786 (pt) cc_final: 0.7480 (mm) REVERT: A 274 TRP cc_start: 0.7670 (t-100) cc_final: 0.7297 (t-100) REVERT: B 83 LEU cc_start: 0.6785 (tp) cc_final: 0.6381 (tp) REVERT: B 243 LEU cc_start: 0.6797 (mp) cc_final: 0.6499 (mm) REVERT: B 275 TYR cc_start: 0.6404 (t80) cc_final: 0.5586 (t80) REVERT: B 430 ASP cc_start: 0.5472 (m-30) cc_final: 0.5046 (m-30) REVERT: C 259 ASP cc_start: 0.7050 (m-30) cc_final: 0.6752 (m-30) REVERT: C 281 ASN cc_start: 0.8139 (m-40) cc_final: 0.7873 (t0) REVERT: C 463 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7384 (tt0) REVERT: C 613 ASP cc_start: 0.6444 (t0) cc_final: 0.6232 (t0) REVERT: C 630 ILE cc_start: 0.8599 (mt) cc_final: 0.8374 (mt) outliers start: 1 outliers final: 1 residues processed: 231 average time/residue: 0.1468 time to fit residues: 51.7535 Evaluate side-chains 139 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 407 HIS 1 524 ASN 1 739 GLN 11055 ASN 11316 HIS A 168 HIS A 275 ASN B 332 ASN C 346 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.060101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.048858 restraints weight = 361864.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050760 restraints weight = 257414.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052178 restraints weight = 141677.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052125 restraints weight = 107429.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052753 restraints weight = 96892.258| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 17956 Z= 0.153 Angle : 0.738 31.958 24426 Z= 0.330 Chirality : 0.045 0.243 2750 Planarity : 0.005 0.107 3071 Dihedral : 6.172 62.131 2541 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.28 (0.18), residues: 2109 helix: 0.98 (0.17), residues: 982 sheet: -0.41 (0.30), residues: 265 loop : -0.44 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 669 TYR 0.021 0.002 TYR 1 359 PHE 0.027 0.002 PHE 11038 TRP 0.035 0.003 TRP 1 785 HIS 0.007 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (17952) covalent geometry : angle 0.63383 / 0.33 (24414) hydrogen bonds : bond 0.04320 / 2.82 ( 850) hydrogen bonds : angle 5.55772 / 3.94 ( 2413) metal coordination : bond 0.00673 / 0.34 ( 4) metal coordination : angle 17.02507 / 9.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.5954 (mtp) cc_final: 0.5515 (mtp) REVERT: 1 430 MET cc_start: 0.7913 (mtt) cc_final: 0.7173 (mtp) REVERT: 1 1237 LEU cc_start: 0.4979 (tp) cc_final: 0.4397 (tp) REVERT: 1 1351 SER cc_start: 0.9145 (m) cc_final: 0.8914 (t) REVERT: 1 1376 MET cc_start: 0.8000 (tpp) cc_final: 0.7535 (tpp) REVERT: A 141 MET cc_start: 0.5393 (mtm) cc_final: 0.5079 (mtm) REVERT: A 271 LYS cc_start: 0.8853 (tptt) cc_final: 0.8522 (tppt) REVERT: A 274 TRP cc_start: 0.7765 (t-100) cc_final: 0.7092 (t-100) REVERT: A 308 THR cc_start: 0.6891 (p) cc_final: 0.6663 (t) REVERT: B 83 LEU cc_start: 0.6968 (tp) cc_final: 0.6711 (tp) REVERT: B 157 LYS cc_start: 0.8434 (mttt) cc_final: 0.7821 (tptm) REVERT: B 243 LEU cc_start: 0.6752 (mp) cc_final: 0.6529 (mm) REVERT: B 256 LEU cc_start: 0.6919 (tp) cc_final: 0.6620 (tp) REVERT: B 430 ASP cc_start: 0.5415 (m-30) cc_final: 0.4917 (m-30) REVERT: B 503 TYR cc_start: 0.5781 (t80) cc_final: 0.5461 (t80) REVERT: C 281 ASN cc_start: 0.8219 (m-40) cc_final: 0.7934 (t0) REVERT: C 613 ASP cc_start: 0.6629 (t0) cc_final: 0.6292 (t0) REVERT: C 616 TYR cc_start: 0.8093 (m-80) cc_final: 0.7504 (m-10) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1327 time to fit residues: 34.8520 Evaluate side-chains 134 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 176 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 191 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 576 ASN 1 653 HIS 1 681 ASN 11055 ASN A 60 ASN A 275 ASN C 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.048045 restraints weight = 352334.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.050074 restraints weight = 257023.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051552 restraints weight = 136930.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.051452 restraints weight = 98728.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051844 restraints weight = 97379.598| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17956 Z= 0.189 Angle : 0.755 31.825 24426 Z= 0.338 Chirality : 0.045 0.233 2750 Planarity : 0.005 0.075 3071 Dihedral : 6.145 64.015 2541 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.17 (0.18), residues: 2109 helix: 0.95 (0.16), residues: 982 sheet: -0.50 (0.30), residues: 258 loop : -0.57 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 1 669 TYR 0.028 0.002 TYR A 117 PHE 0.025 0.003 PHE B 75 TRP 0.028 0.003 TRP B 78 HIS 0.007 0.002 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (17952) covalent geometry : angle 0.65318 / 0.34 (24414) hydrogen bonds : bond 0.04253 / 2.81 ( 850) hydrogen bonds : angle 5.41768 / 3.83 ( 2413) metal coordination : bond 0.00672 / 0.34 ( 4) metal coordination : angle 17.11082 / 9.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6118 (mtp) cc_final: 0.5713 (mtp) REVERT: 1 430 MET cc_start: 0.7913 (mtt) cc_final: 0.7169 (mtp) REVERT: 1 1237 LEU cc_start: 0.5058 (tp) cc_final: 0.4322 (tp) REVERT: 1 1351 SER cc_start: 0.9140 (m) cc_final: 0.8898 (t) REVERT: 1 1376 MET cc_start: 0.8031 (tpp) cc_final: 0.7554 (tpp) REVERT: A 271 LYS cc_start: 0.8826 (tptt) cc_final: 0.8503 (tppt) REVERT: A 274 TRP cc_start: 0.7738 (t-100) cc_final: 0.7065 (t-100) REVERT: A 308 THR cc_start: 0.6949 (p) cc_final: 0.6726 (t) REVERT: B 83 LEU cc_start: 0.6880 (tp) cc_final: 0.6582 (tp) REVERT: B 157 LYS cc_start: 0.8411 (mttt) cc_final: 0.7916 (tptt) REVERT: B 256 LEU cc_start: 0.6882 (tp) cc_final: 0.6564 (tp) REVERT: B 470 TYR cc_start: 0.3476 (m-10) cc_final: 0.3129 (m-10) REVERT: C 281 ASN cc_start: 0.8346 (m-40) cc_final: 0.7993 (t0) REVERT: C 631 MET cc_start: 0.4367 (ptm) cc_final: 0.4131 (ptm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1226 time to fit residues: 32.3908 Evaluate side-chains 127 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 120 optimal weight: 0.0060 chunk 43 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 11055 ASN 11359 GLN B 257 ASN C 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.048548 restraints weight = 312261.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050250 restraints weight = 211103.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051515 restraints weight = 124034.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051639 restraints weight = 92104.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051836 restraints weight = 85980.683| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17956 Z= 0.156 Angle : 0.711 30.816 24426 Z= 0.312 Chirality : 0.044 0.196 2750 Planarity : 0.005 0.066 3071 Dihedral : 6.029 64.834 2541 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.27 (0.18), residues: 2109 helix: 1.09 (0.17), residues: 983 sheet: -0.49 (0.31), residues: 254 loop : -0.56 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 669 TYR 0.017 0.002 TYR B 275 PHE 0.028 0.002 PHE C 454 TRP 0.028 0.002 TRP B 376 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (17952) covalent geometry : angle 0.60634 / 0.31 (24414) hydrogen bonds : bond 0.03868 / 2.53 ( 850) hydrogen bonds : angle 5.26424 / 3.73 ( 2413) metal coordination : bond 0.02455 / 1.28 ( 4) metal coordination : angle 16.75384 / 9.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6082 (mtp) cc_final: 0.5776 (mtp) REVERT: 1 430 MET cc_start: 0.7908 (mtt) cc_final: 0.7198 (mtp) REVERT: 1 619 MET cc_start: 0.7601 (ttp) cc_final: 0.7096 (ttt) REVERT: 1 1237 LEU cc_start: 0.5032 (tp) cc_final: 0.4176 (tp) REVERT: 1 1351 SER cc_start: 0.9138 (m) cc_final: 0.8894 (t) REVERT: 1 1376 MET cc_start: 0.7964 (tpp) cc_final: 0.7539 (tpp) REVERT: A 20 LYS cc_start: 0.8376 (tttt) cc_final: 0.8112 (ttmm) REVERT: A 114 MET cc_start: 0.7183 (mmt) cc_final: 0.6816 (mmm) REVERT: A 271 LYS cc_start: 0.8626 (tptt) cc_final: 0.8404 (tppt) REVERT: A 274 TRP cc_start: 0.7680 (t-100) cc_final: 0.7122 (t-100) REVERT: B 83 LEU cc_start: 0.6910 (tp) cc_final: 0.6579 (tp) REVERT: B 157 LYS cc_start: 0.8341 (mttt) cc_final: 0.7798 (tptt) REVERT: B 256 LEU cc_start: 0.6854 (tp) cc_final: 0.6500 (tp) REVERT: B 451 MET cc_start: 0.6972 (mtm) cc_final: 0.6768 (mmt) REVERT: B 470 TYR cc_start: 0.3454 (m-10) cc_final: 0.3109 (m-10) REVERT: C 281 ASN cc_start: 0.8333 (m-40) cc_final: 0.7926 (t0) REVERT: C 631 MET cc_start: 0.4400 (ptm) cc_final: 0.4189 (ptm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1200 time to fit residues: 29.6787 Evaluate side-chains 128 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 121 optimal weight: 10.0000 chunk 183 optimal weight: 0.0470 chunk 144 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 11055 ASN A 71 GLN B 257 ASN B 441 HIS C 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.058907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.047754 restraints weight = 368849.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.049946 restraints weight = 258305.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051322 restraints weight = 133113.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051310 restraints weight = 96572.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.051642 restraints weight = 95760.451| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17956 Z= 0.196 Angle : 0.758 29.255 24426 Z= 0.337 Chirality : 0.046 0.196 2750 Planarity : 0.005 0.061 3071 Dihedral : 6.242 66.513 2541 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.18), residues: 2109 helix: 0.90 (0.16), residues: 980 sheet: -0.57 (0.31), residues: 251 loop : -0.65 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 1 669 TYR 0.020 0.002 TYR B 275 PHE 0.025 0.003 PHE B 75 TRP 0.032 0.002 TRP B 376 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (17952) covalent geometry : angle 0.65423 / 0.34 (24414) hydrogen bonds : bond 0.04100 / 2.70 ( 850) hydrogen bonds : angle 5.38043 / 3.80 ( 2413) metal coordination : bond 0.01285 / 0.67 ( 4) metal coordination : angle 17.30663 / 9.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6179 (mtp) cc_final: 0.5925 (mtp) REVERT: 1 430 MET cc_start: 0.7853 (mtt) cc_final: 0.7162 (mtp) REVERT: 1 1237 LEU cc_start: 0.5172 (tp) cc_final: 0.4280 (tp) REVERT: 1 1351 SER cc_start: 0.9132 (m) cc_final: 0.8886 (t) REVERT: 1 1376 MET cc_start: 0.7939 (tpp) cc_final: 0.7450 (tpp) REVERT: A 271 LYS cc_start: 0.8619 (tptt) cc_final: 0.8389 (tppt) REVERT: A 274 TRP cc_start: 0.7736 (t-100) cc_final: 0.6853 (t60) REVERT: B 157 LYS cc_start: 0.8284 (mttt) cc_final: 0.7762 (tptt) REVERT: B 256 LEU cc_start: 0.6832 (tp) cc_final: 0.6447 (tp) REVERT: B 451 MET cc_start: 0.7017 (mtm) cc_final: 0.6757 (mmt) REVERT: B 470 TYR cc_start: 0.3411 (m-10) cc_final: 0.3040 (m-10) REVERT: C 281 ASN cc_start: 0.8341 (m-40) cc_final: 0.7869 (t0) REVERT: C 378 SER cc_start: 0.8421 (p) cc_final: 0.7521 (t) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1203 time to fit residues: 31.5310 Evaluate side-chains 132 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 17 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 142 optimal weight: 0.5980 chunk 144 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 11055 ASN 11359 GLN 11404 GLN B 257 ASN B 332 ASN B 441 HIS ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.057989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.047606 restraints weight = 296963.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.048978 restraints weight = 216004.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049879 restraints weight = 139147.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.050286 restraints weight = 104486.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.050764 restraints weight = 92797.901| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 17956 Z= 0.265 Angle : 0.880 30.489 24426 Z= 0.400 Chirality : 0.050 0.244 2750 Planarity : 0.006 0.060 3071 Dihedral : 6.854 69.582 2541 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.11 % Allowed : 2.29 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.18), residues: 2109 helix: 0.36 (0.16), residues: 963 sheet: -0.87 (0.31), residues: 251 loop : -1.00 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 1 669 TYR 0.033 0.003 TYR B 55 PHE 0.044 0.003 PHE B 61 TRP 0.044 0.003 TRP B 376 HIS 0.009 0.002 HIS C 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.27 (17952) covalent geometry : angle 0.78258 / 0.40 (24414) hydrogen bonds : bond 0.04705 / 3.12 ( 850) hydrogen bonds : angle 5.80431 / 4.08 ( 2413) metal coordination : bond 0.01051 / 0.53 ( 4) metal coordination : angle 18.20179 / 10.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 430 MET cc_start: 0.7706 (mtt) cc_final: 0.7014 (mtp) REVERT: 1 619 MET cc_start: 0.7658 (ttp) cc_final: 0.7179 (ttt) REVERT: 1 633 ASP cc_start: 0.6625 (m-30) cc_final: 0.5900 (t0) REVERT: 1 747 MET cc_start: 0.8011 (tpt) cc_final: 0.7637 (tpt) REVERT: 1 956 TYR cc_start: 0.5735 (m-80) cc_final: 0.5466 (m-80) REVERT: 1 1121 ASN cc_start: 0.7092 (t0) cc_final: 0.6882 (t0) REVERT: 1 1237 LEU cc_start: 0.5120 (tp) cc_final: 0.4151 (tp) REVERT: 1 1376 MET cc_start: 0.7995 (tpp) cc_final: 0.7432 (tpp) REVERT: A 20 LYS cc_start: 0.8441 (tttt) cc_final: 0.8180 (ttmm) REVERT: A 271 LYS cc_start: 0.8672 (tptt) cc_final: 0.8426 (tppt) REVERT: A 274 TRP cc_start: 0.7761 (t-100) cc_final: 0.6752 (t60) REVERT: B 116 PHE cc_start: 0.6484 (p90) cc_final: 0.6187 (p90) REVERT: B 157 LYS cc_start: 0.8224 (mttt) cc_final: 0.7736 (tptt) REVERT: B 256 LEU cc_start: 0.6829 (tp) cc_final: 0.6491 (tp) REVERT: C 259 ASP cc_start: 0.7074 (m-30) cc_final: 0.6788 (m-30) REVERT: C 281 ASN cc_start: 0.8314 (m-40) cc_final: 0.8100 (m-40) REVERT: C 613 ASP cc_start: 0.6929 (t0) cc_final: 0.6675 (t0) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1242 time to fit residues: 30.9933 Evaluate side-chains 127 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 23 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 11055 ASN 11404 GLN B 257 ASN C 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.048597 restraints weight = 296869.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.049861 restraints weight = 212643.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.050824 restraints weight = 142133.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051416 restraints weight = 103759.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.051776 restraints weight = 89671.751| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17956 Z= 0.166 Angle : 0.747 30.475 24426 Z= 0.327 Chirality : 0.045 0.260 2750 Planarity : 0.005 0.057 3071 Dihedral : 6.464 68.696 2541 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.05 % Allowed : 1.17 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.24 (0.18), residues: 2109 helix: 0.69 (0.16), residues: 982 sheet: -0.73 (0.32), residues: 246 loop : -0.87 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 149 TYR 0.034 0.002 TYR B 333 PHE 0.025 0.002 PHE B 75 TRP 0.047 0.002 TRP B 376 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (17952) covalent geometry : angle 0.64068 / 0.33 (24414) hydrogen bonds : bond 0.04037 / 2.66 ( 850) hydrogen bonds : angle 5.44322 / 3.84 ( 2413) metal coordination : bond 0.00763 / 0.37 ( 4) metal coordination : angle 17.37508 / 9.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 619 MET cc_start: 0.7552 (ttp) cc_final: 0.7045 (ttt) REVERT: 1 747 MET cc_start: 0.8010 (tpt) cc_final: 0.7751 (tpt) REVERT: 1 956 TYR cc_start: 0.5849 (m-80) cc_final: 0.5582 (m-80) REVERT: 1 1237 LEU cc_start: 0.5080 (tp) cc_final: 0.4125 (tp) REVERT: 1 1351 SER cc_start: 0.9142 (m) cc_final: 0.8891 (t) REVERT: A 20 LYS cc_start: 0.8488 (tttt) cc_final: 0.7993 (tppt) REVERT: A 114 MET cc_start: 0.7050 (mmt) cc_final: 0.6831 (mmt) REVERT: A 271 LYS cc_start: 0.8669 (tptt) cc_final: 0.8447 (tppt) REVERT: A 274 TRP cc_start: 0.7788 (t-100) cc_final: 0.7391 (t-100) REVERT: B 83 LEU cc_start: 0.6981 (tp) cc_final: 0.6548 (tt) REVERT: B 116 PHE cc_start: 0.6424 (p90) cc_final: 0.6207 (p90) REVERT: B 157 LYS cc_start: 0.8190 (mttt) cc_final: 0.7679 (tptt) REVERT: B 256 LEU cc_start: 0.6790 (tp) cc_final: 0.6496 (tp) REVERT: B 451 MET cc_start: 0.7058 (mtm) cc_final: 0.6776 (mmt) REVERT: B 470 TYR cc_start: 0.3595 (m-10) cc_final: 0.3365 (m-10) REVERT: C 259 ASP cc_start: 0.7065 (m-30) cc_final: 0.6793 (m-30) REVERT: C 281 ASN cc_start: 0.8297 (m-40) cc_final: 0.8062 (m-40) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1235 time to fit residues: 31.1177 Evaluate side-chains 131 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 209 optimal weight: 0.2980 chunk 204 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 61 optimal weight: 0.0070 chunk 96 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 11404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.060106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.049212 restraints weight = 316784.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.051122 restraints weight = 213047.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052519 restraints weight = 118669.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052550 restraints weight = 87762.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.052934 restraints weight = 81708.251| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17956 Z= 0.118 Angle : 0.679 30.416 24426 Z= 0.295 Chirality : 0.043 0.276 2750 Planarity : 0.004 0.055 3071 Dihedral : 5.993 65.702 2541 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.29 (0.18), residues: 2109 helix: 1.21 (0.17), residues: 975 sheet: -0.59 (0.32), residues: 245 loop : -0.65 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 506 TYR 0.017 0.001 TYR B 503 PHE 0.021 0.002 PHE B 75 TRP 0.041 0.002 TRP B 376 HIS 0.004 0.001 HIS 1 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (17952) covalent geometry : angle 0.58014 / 0.29 (24414) hydrogen bonds : bond 0.03599 / 2.36 ( 850) hydrogen bonds : angle 5.07833 / 3.60 ( 2413) metal coordination : bond 0.00386 / 0.18 ( 4) metal coordination : angle 15.96135 / 9.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 619 MET cc_start: 0.7490 (ttp) cc_final: 0.7224 (ttp) REVERT: 1 954 LEU cc_start: 0.7907 (pp) cc_final: 0.7572 (tt) REVERT: 1 956 TYR cc_start: 0.5885 (m-80) cc_final: 0.5580 (m-80) REVERT: 1 1237 LEU cc_start: 0.4963 (tp) cc_final: 0.4041 (tp) REVERT: 1 1351 SER cc_start: 0.9067 (m) cc_final: 0.8811 (t) REVERT: A 20 LYS cc_start: 0.8462 (tttt) cc_final: 0.7963 (tppt) REVERT: A 271 LYS cc_start: 0.8670 (tptt) cc_final: 0.8428 (tppt) REVERT: A 274 TRP cc_start: 0.7760 (t-100) cc_final: 0.7325 (t-100) REVERT: B 83 LEU cc_start: 0.6762 (tp) cc_final: 0.6475 (tp) REVERT: B 157 LYS cc_start: 0.8217 (mttt) cc_final: 0.7659 (tptm) REVERT: B 243 LEU cc_start: 0.6224 (mm) cc_final: 0.5917 (mt) REVERT: B 256 LEU cc_start: 0.6709 (tp) cc_final: 0.6344 (tp) REVERT: B 333 TYR cc_start: 0.4215 (m-10) cc_final: 0.3988 (m-10) REVERT: B 451 MET cc_start: 0.7026 (mtm) cc_final: 0.6730 (mmt) REVERT: B 470 TYR cc_start: 0.3288 (m-10) cc_final: 0.2974 (m-10) REVERT: C 259 ASP cc_start: 0.7112 (m-30) cc_final: 0.6892 (m-30) REVERT: C 281 ASN cc_start: 0.8340 (m-40) cc_final: 0.7906 (t0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1211 time to fit residues: 31.9222 Evaluate side-chains 131 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 213 optimal weight: 30.0000 chunk 189 optimal weight: 8.9990 chunk 125 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 11055 ASN ** 11404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN B 347 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.047678 restraints weight = 277240.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.048849 restraints weight = 189632.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.049791 restraints weight = 130103.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049956 restraints weight = 101718.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.050312 restraints weight = 97050.156| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 17956 Z= 0.306 Angle : 0.921 30.820 24426 Z= 0.425 Chirality : 0.052 0.278 2750 Planarity : 0.006 0.074 3071 Dihedral : 6.985 69.617 2541 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.05 % Allowed : 0.96 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.65 (0.18), residues: 2109 helix: 0.31 (0.16), residues: 965 sheet: -0.98 (0.33), residues: 223 loop : -1.01 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 135 TYR 0.030 0.003 TYR B 275 PHE 0.036 0.004 PHE B 61 TRP 0.057 0.003 TRP B 376 HIS 0.011 0.002 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.31 (17952) covalent geometry : angle 0.82858 / 0.42 (24414) hydrogen bonds : bond 0.04918 / 3.26 ( 850) hydrogen bonds : angle 5.85545 / 4.10 ( 2413) metal coordination : bond 0.01375 / 0.70 ( 4) metal coordination : angle 18.11259 / 10.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 633 ASP cc_start: 0.6580 (m-30) cc_final: 0.5845 (t0) REVERT: 1 956 TYR cc_start: 0.5790 (m-80) cc_final: 0.5568 (m-80) REVERT: 1 994 TYR cc_start: 0.6444 (t80) cc_final: 0.5823 (t80) REVERT: 1 1121 ASN cc_start: 0.7056 (t0) cc_final: 0.6836 (t0) REVERT: 1 1237 LEU cc_start: 0.5045 (tp) cc_final: 0.3979 (tp) REVERT: A 20 LYS cc_start: 0.8378 (tttt) cc_final: 0.8141 (ttmm) REVERT: A 271 LYS cc_start: 0.8591 (tptt) cc_final: 0.8201 (tppt) REVERT: B 116 PHE cc_start: 0.6570 (p90) cc_final: 0.6088 (p90) REVERT: B 157 LYS cc_start: 0.8255 (mttt) cc_final: 0.7703 (tptm) REVERT: B 243 LEU cc_start: 0.6415 (mm) cc_final: 0.6067 (mt) REVERT: B 256 LEU cc_start: 0.6836 (tp) cc_final: 0.6613 (tp) REVERT: B 451 MET cc_start: 0.7003 (mtm) cc_final: 0.6699 (mmt) REVERT: C 252 GLN cc_start: 0.6810 (pt0) cc_final: 0.6358 (pt0) REVERT: C 259 ASP cc_start: 0.7088 (m-30) cc_final: 0.6846 (m-30) REVERT: C 560 VAL cc_start: 0.8786 (t) cc_final: 0.8534 (p) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1202 time to fit residues: 27.3026 Evaluate side-chains 125 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 212 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 11404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048976 restraints weight = 298096.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050351 restraints weight = 212192.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051445 restraints weight = 136838.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051538 restraints weight = 105223.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.052206 restraints weight = 95215.703| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17956 Z= 0.137 Angle : 0.724 31.219 24426 Z= 0.314 Chirality : 0.044 0.288 2750 Planarity : 0.004 0.056 3071 Dihedral : 6.319 66.977 2541 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.05 % Allowed : 0.48 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.11 (0.18), residues: 2109 helix: 0.84 (0.17), residues: 981 sheet: -0.84 (0.34), residues: 214 loop : -0.82 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 1 669 TYR 0.016 0.001 TYR B 129 PHE 0.024 0.002 PHE B 75 TRP 0.018 0.002 TRP 1 714 HIS 0.004 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (17952) covalent geometry : angle 0.62312 / 0.31 (24414) hydrogen bonds : bond 0.03827 / 2.52 ( 850) hydrogen bonds : angle 5.28546 / 3.72 ( 2413) metal coordination : bond 0.00563 / 0.28 ( 4) metal coordination : angle 16.68323 / 9.53 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 956 TYR cc_start: 0.5938 (m-80) cc_final: 0.5686 (m-80) REVERT: 1 1237 LEU cc_start: 0.4992 (tp) cc_final: 0.4026 (tp) REVERT: 1 1351 SER cc_start: 0.9092 (m) cc_final: 0.8829 (t) REVERT: A 20 LYS cc_start: 0.8449 (tttt) cc_final: 0.8094 (tppt) REVERT: A 271 LYS cc_start: 0.8603 (tptt) cc_final: 0.8287 (tppt) REVERT: B 83 LEU cc_start: 0.6680 (tp) cc_final: 0.6375 (tp) REVERT: B 110 PHE cc_start: 0.5684 (m-10) cc_final: 0.5369 (m-10) REVERT: B 116 PHE cc_start: 0.6434 (p90) cc_final: 0.5940 (p90) REVERT: B 157 LYS cc_start: 0.8156 (mttt) cc_final: 0.7650 (tptm) REVERT: B 243 LEU cc_start: 0.6243 (mm) cc_final: 0.5903 (mt) REVERT: B 256 LEU cc_start: 0.6696 (tp) cc_final: 0.6374 (tp) REVERT: B 333 TYR cc_start: 0.4117 (m-10) cc_final: 0.3913 (m-10) REVERT: B 451 MET cc_start: 0.7009 (mtm) cc_final: 0.6524 (mmm) REVERT: B 470 TYR cc_start: 0.3541 (m-10) cc_final: 0.3222 (m-10) REVERT: C 281 ASN cc_start: 0.8314 (m-40) cc_final: 0.8083 (m-40) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1165 time to fit residues: 28.2681 Evaluate side-chains 124 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 75 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 11404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.048680 restraints weight = 290496.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.050005 restraints weight = 203087.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051097 restraints weight = 133206.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.051480 restraints weight = 98059.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051850 restraints weight = 86361.999| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17956 Z= 0.169 Angle : 0.742 30.760 24426 Z= 0.325 Chirality : 0.045 0.286 2750 Planarity : 0.005 0.055 3071 Dihedral : 6.354 66.739 2541 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.12 (0.18), residues: 2109 helix: 0.84 (0.17), residues: 975 sheet: -0.96 (0.34), residues: 214 loop : -0.79 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 1 669 TYR 0.019 0.002 TYR B 275 PHE 0.023 0.002 PHE B 75 TRP 0.036 0.002 TRP B 376 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (17952) covalent geometry : angle 0.64147 / 0.32 (24414) hydrogen bonds : bond 0.03948 / 2.60 ( 850) hydrogen bonds : angle 5.33086 / 3.75 ( 2413) metal coordination : bond 0.00733 / 0.37 ( 4) metal coordination : angle 16.84730 / 9.61 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2563.51 seconds wall clock time: 45 minutes 21.96 seconds (2721.96 seconds total)