Starting phenix.real_space_refine on Sun Jun 15 06:31:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8foh_29349/06_2025/8foh_29349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foh_29349/06_2025/8foh_29349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8foh_29349/06_2025/8foh_29349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foh_29349/06_2025/8foh_29349.map" model { file = "/net/cci-nas-00/data/ceres_data/8foh_29349/06_2025/8foh_29349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foh_29349/06_2025/8foh_29349.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 20 5.49 5 S 93 5.16 5 C 10746 2.51 5 N 2926 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16996 Number of models: 1 Model: "" Number of chains: 7 Chain: "1" Number of atoms: 7136 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 893, 7128 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 41, 'TRANS': 851} Chain breaks: 12 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 893, 7128 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 41, 'TRANS': 851} Chain breaks: 12 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 7245 Chain: "A" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2780 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 3381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3358 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 406, 3358 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 3402 Chain: "C" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3255 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 5, 'PTRANS': 23, 'TRANS': 381} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 410, 3255 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 5, 'PTRANS': 23, 'TRANS': 381} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3308 Chain: "T" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 241 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "P" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} 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 12081 SG CYS B 336 85.739 58.913 110.097 1.00 16.40 S ATOM 12802 SG CYS B 434 84.469 61.343 104.265 1.00 18.69 S ATOM 12670 SG CYS B 417 85.146 54.838 105.091 1.00 17.89 S ATOM 13072 SG CYS B 474 90.063 58.277 105.062 1.00 16.49 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASP 11414 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.50 residue: pdb=" N AASP C 263 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.50 residue: pdb=" N AHIS C 495 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 495 " occ=0.50 Time building chain proxies: 15.41, per 1000 atoms: 0.91 Number of scatterers: 16996 At special positions: 0 Unit cell: (111.78, 119.232, 197.892, 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 93 16.00 P 20 15.00 O 3207 8.00 N 2926 7.00 C 10746 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: 4.15 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " Number of angles added : 12 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 17 sheets defined 51.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 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 525 Processing helix chain '1' and resid 615 through 631 Processing helix chain '1' and resid 643 through 655 Processing helix chain '1' and resid 659 through 664 Processing helix chain '1' and resid 679 through 692 removed outlier: 3.747A pdb=" N HIS 1 684 " --> pdb=" O SER 1 680 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE 1 685 " --> pdb=" O ASN 1 681 " (cutoff:3.500A) Processing helix chain '1' and resid 701 through 707 removed outlier: 3.678A 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 738 through 743 removed outlier: 4.118A pdb=" N ASN 1 742 " --> pdb=" O PRO 1 738 " (cutoff:3.500A) Processing helix chain '1' and resid 743 through 768 Processing helix chain '1' and resid 769 through 782 Processing helix chain '1' and resid 784 through 791 Processing helix chain '1' and resid 795 through 808 removed outlier: 3.554A pdb=" N TYR 1 799 " --> pdb=" O GLY 1 795 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE 1 800 " --> pdb=" O ARG 1 796 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU 1 801 " --> pdb=" O ASN 1 797 " (cutoff:3.500A) Processing helix chain '1' and resid 867 through 876 removed outlier: 3.608A pdb=" N SER 1 871 " --> pdb=" O SER 1 867 " (cutoff:3.500A) Processing helix chain '1' and resid 906 through 927 removed outlier: 3.711A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 929 through 948 Processing helix chain '1' and resid 950 through 956 removed outlier: 4.163A pdb=" N LEU 1 954 " --> pdb=" O MET 1 950 " (cutoff:3.500A) 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 1080 through 1094 Processing helix chain '1' and resid 1102 through 1119 removed outlier: 3.527A pdb=" N ASP 11112 " --> pdb=" O ASP 11108 " (cutoff:3.500A) Processing helix chain '1' and resid 1211 through 1216 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 1344 removed outlier: 4.263A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY 11344 " --> pdb=" O LEU 11340 " (cutoff:3.500A) Processing helix chain '1' and resid 1381 through 1396 removed outlier: 3.818A pdb=" N PHE 11396 " --> pdb=" O PHE 11392 " (cutoff:3.500A) Processing helix chain '1' and resid 1397 through 1403 Processing helix chain '1' and resid 1423 through 1434 Processing helix chain '1' and resid 1434 through 1450 removed outlier: 3.608A pdb=" N VAL 11445 " --> pdb=" O GLY 11441 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 114 through 121 removed outlier: 5.101A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 151 removed outlier: 3.645A pdb=" N LYS A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 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: 4.366A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.845A 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 246 through 249 Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 269 through 285 removed outlier: 4.061A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.809A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.280A 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 353 through 358 Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 74 through 95 Processing helix chain 'B' and resid 98 through 114 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 120 through 139 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 208 removed outlier: 4.664A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.575A pdb=" N GLN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.597A 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 298 removed outlier: 3.684A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix 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 365 Processing helix chain 'B' and resid 368 through 380 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.628A pdb=" N TYR B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) 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 449 Processing helix chain 'B' and resid 457 through 467 Processing helix chain 'B' and resid 469 through 482 Processing helix chain 'B' and resid 499 through 510 Processing helix chain 'C' and resid 253 through 277 removed outlier: 3.684A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 321 through 326 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 446 Processing helix chain 'C' and resid 460 through 469 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 548 through 554 Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 613 through 621 removed outlier: 4.996A 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 Processing sheet with id=AA1, first strand: chain '1' and resid 515 through 519 removed outlier: 6.868A pdb=" N SER 1 381 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL 1 517 " --> pdb=" O SER 1 381 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N MET 1 383 " --> pdb=" O VAL 1 517 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL 1 519 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 519 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 1 366 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS 1 371 " --> pdb=" O TRP 1 356 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP 1 356 " --> pdb=" O LYS 1 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 425 through 431 removed outlier: 7.262A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 609 through 612 removed outlier: 6.781A pdb=" N LEU 1 582 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARG 1 611 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR 1 584 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN 1 544 " --> pdb=" O VAL 1 557 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE 1 559 " --> pdb=" O SER 1 542 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER 1 542 " --> pdb=" O ILE 1 559 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU 1 561 " --> pdb=" O SER 1 540 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER 1 540 " --> pdb=" O LEU 1 561 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA 1 563 " --> pdb=" O CYS 1 538 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS 1 538 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG 1 565 " --> pdb=" O LEU 1 536 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU 1 536 " --> pdb=" O ARG 1 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 854 through 856 removed outlier: 6.664A pdb=" N ILE 11034 " --> pdb=" O ASP 1 864 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP 1 864 " --> pdb=" O ILE 11034 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER 1 999 " --> pdb=" O GLY 1 995 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY 1 995 " --> pdb=" O SER 1 999 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET 11001 " --> pdb=" O VAL 1 993 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU 1 991 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 854 through 856 removed outlier: 13.471A pdb=" N ASP 11035 " --> pdb=" O LEU 11056 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N LEU 11056 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL 11037 " --> pdb=" O VAL 11054 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU 11052 " --> pdb=" O LYS 11039 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU 11041 " --> pdb=" O ALA 11050 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA 11050 " --> pdb=" O LEU 11041 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU 11043 " --> pdb=" O LYS 11048 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LYS 11048 " --> pdb=" O LEU 11043 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 1283 through 1286 removed outlier: 4.665A pdb=" N LEU 11283 " --> pdb=" O PHE 11296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 1305 through 1308 Processing sheet with id=AA8, first strand: chain '1' and resid 1356 through 1357 Processing sheet with id=AA9, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.505A pdb=" N TYR A 59 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 47 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 157 through 161 removed outlier: 4.559A pdb=" N ASP A 111 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 181 through 182 removed outlier: 4.071A pdb=" N GLN B 181 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AB4, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB5, first strand: chain 'C' and resid 375 through 376 Processing sheet with id=AB6, first strand: chain 'C' and resid 515 through 517 removed outlier: 6.310A pdb=" N THR C 482 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS C 394 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE C 430 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE C 396 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE C 432 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR C 398 " --> pdb=" O PHE C 432 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.407A pdb=" N TYR C 530 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE C 632 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY C 532 " --> pdb=" O ILE C 632 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 578 through 579 839 hydrogen bonds defined for protein. 2356 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: 6.20 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.42: 7193 1.42 - 1.65: 10067 1.65 - 1.89: 129 1.89 - 2.13: 0 2.13 - 2.37: 12 Bond restraints: 17401 Sorted by residual: bond pdb=" C1' C P 4 " pdb=" N1 C P 4 " ideal model delta sigma weight residual 1.480 1.579 -0.099 1.50e-02 4.44e+03 4.32e+01 bond pdb=" C1' C P 8 " pdb=" N1 C P 8 " ideal model delta sigma weight residual 1.480 1.577 -0.097 1.50e-02 4.44e+03 4.17e+01 bond pdb=" CA VAL C 623 " pdb=" CB VAL C 623 " ideal model delta sigma weight residual 1.536 1.597 -0.061 1.16e-02 7.43e+03 2.75e+01 bond pdb=" C PRO 11408 " pdb=" O PRO 11408 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.10e-02 8.26e+03 2.44e+01 bond pdb=" CA ASN C 693 " pdb=" C ASN C 693 " ideal model delta sigma weight residual 1.527 1.463 0.064 1.32e-02 5.74e+03 2.35e+01 ... (remaining 17396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 21912 2.63 - 5.26: 1591 5.26 - 7.90: 91 7.90 - 10.53: 6 10.53 - 13.16: 26 Bond angle restraints: 23626 Sorted by residual: angle pdb=" O3' G P 6 " pdb=" P G P 7 " pdb=" O5' G P 7 " ideal model delta sigma weight residual 104.00 91.04 12.96 1.50e+00 4.44e-01 7.46e+01 angle pdb=" O3' C P 4 " pdb=" P G P 5 " pdb=" O5' G P 5 " ideal model delta sigma weight residual 104.00 91.06 12.94 1.50e+00 4.44e-01 7.45e+01 angle pdb=" O3' DC T 17 " pdb=" P DC T 18 " pdb=" O5' DC T 18 " ideal model delta sigma weight residual 104.00 91.07 12.93 1.50e+00 4.44e-01 7.44e+01 angle pdb=" O3' G P 7 " pdb=" P C P 8 " pdb=" O5' C P 8 " ideal model delta sigma weight residual 104.00 91.10 12.90 1.50e+00 4.44e-01 7.40e+01 angle pdb=" O3' G P 5 " pdb=" P G P 6 " pdb=" O5' G P 6 " ideal model delta sigma weight residual 104.00 91.12 12.88 1.50e+00 4.44e-01 7.37e+01 ... (remaining 23621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 9753 17.58 - 35.17: 640 35.17 - 52.75: 124 52.75 - 70.33: 39 70.33 - 87.91: 17 Dihedral angle restraints: 10573 sinusoidal: 4505 harmonic: 6068 Sorted by residual: dihedral pdb=" C ASP C 303 " pdb=" N ASP C 303 " pdb=" CA ASP C 303 " pdb=" CB ASP C 303 " ideal model delta harmonic sigma weight residual -122.60 -137.15 14.55 0 2.50e+00 1.60e-01 3.39e+01 dihedral pdb=" N ASP C 303 " pdb=" C ASP C 303 " pdb=" CA ASP C 303 " pdb=" CB ASP C 303 " ideal model delta harmonic sigma weight residual 122.80 135.25 -12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA ARG C 579 " pdb=" C ARG C 579 " pdb=" N THR C 580 " pdb=" CA THR C 580 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 10570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2375 0.140 - 0.280: 223 0.280 - 0.419: 17 0.419 - 0.559: 9 0.559 - 0.699: 2 Chirality restraints: 2626 Sorted by residual: chirality pdb="FE1 SF4 B 601 " pdb=" S2 SF4 B 601 " pdb=" S3 SF4 B 601 " pdb=" S4 SF4 B 601 " both_signs ideal model delta sigma weight residual False -10.55 -11.25 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" P DG T 10 " pdb=" OP1 DG T 10 " pdb=" OP2 DG T 10 " pdb=" O5' DG T 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA ASP C 303 " pdb=" N ASP C 303 " pdb=" C ASP C 303 " pdb=" CB ASP C 303 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.71e+00 ... (remaining 2623 not shown) Planarity restraints: 2972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 55 " 0.188 2.00e-02 2.50e+03 1.34e-01 3.60e+02 pdb=" CG TYR B 55 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR B 55 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR B 55 " -0.106 2.00e-02 2.50e+03 pdb=" CE1 TYR B 55 " -0.148 2.00e-02 2.50e+03 pdb=" CE2 TYR B 55 " -0.090 2.00e-02 2.50e+03 pdb=" CZ TYR B 55 " -0.048 2.00e-02 2.50e+03 pdb=" OH TYR B 55 " 0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 209 " -0.140 2.00e-02 2.50e+03 7.32e-02 1.07e+02 pdb=" CG TYR A 209 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 209 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 209 " 0.083 2.00e-02 2.50e+03 pdb=" CE1 TYR A 209 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR A 209 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 209 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 209 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 51 " -0.123 2.00e-02 2.50e+03 6.98e-02 9.75e+01 pdb=" CG TYR B 51 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 51 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR B 51 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR B 51 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR B 51 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR B 51 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 51 " -0.104 2.00e-02 2.50e+03 ... (remaining 2969 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 4 2.14 - 2.83: 4626 2.83 - 3.52: 23528 3.52 - 4.21: 40842 4.21 - 4.90: 69685 Nonbonded interactions: 138685 Sorted by model distance: nonbonded pdb=" N1 DG T 16 " pdb=" N1 G P 6 " model vdw 1.447 3.200 nonbonded pdb=" N2 DG T 16 " pdb=" N2 G P 6 " model vdw 1.565 3.200 nonbonded pdb=" O6 DG T 16 " pdb=" O6 G P 6 " model vdw 1.856 3.040 nonbonded pdb=" N2 DG T 16 " pdb=" C2 G P 6 " model vdw 2.033 3.340 nonbonded pdb=" C2 DG T 16 " pdb=" N2 G P 6 " model vdw 2.151 3.340 ... (remaining 138680 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=0.50 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 50.960 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.110 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 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 : 0.013 0.132 17405 Z= 0.731 Angle : 1.466 13.159 23638 Z= 0.952 Chirality : 0.088 0.699 2626 Planarity : 0.011 0.218 2972 Dihedral : 13.110 87.912 6625 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.61 % Favored : 97.29 % Rotamer: Outliers : 0.49 % Allowed : 3.57 % Favored : 95.94 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2006 helix: -0.26 (0.15), residues: 949 sheet: -0.37 (0.34), residues: 207 loop : -0.03 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.010 TRP B 78 HIS 0.031 0.005 HIS B 348 PHE 0.065 0.007 PHE B 138 TYR 0.250 0.011 TYR B 55 ARG 0.017 0.002 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.16423 ( 835) hydrogen bonds : angle 7.21691 ( 2356) metal coordination : bond 0.02834 ( 4) metal coordination : angle 5.04449 ( 12) covalent geometry : bond 0.01290 (17401) covalent geometry : angle 1.46230 (23626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 652 MET cc_start: 0.8848 (mtt) cc_final: 0.8591 (mtt) REVERT: 1 919 GLU cc_start: 0.9685 (mt-10) cc_final: 0.9442 (mt-10) REVERT: 1 950 MET cc_start: 0.9379 (mmm) cc_final: 0.9077 (mmm) REVERT: 1 1438 MET cc_start: 0.8997 (mmp) cc_final: 0.8757 (mmm) REVERT: A 108 LEU cc_start: 0.9003 (tp) cc_final: 0.8787 (mt) REVERT: A 141 MET cc_start: 0.8933 (mtm) cc_final: 0.8726 (mtm) REVERT: B 128 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8690 (t80) outliers start: 9 outliers final: 0 residues processed: 110 average time/residue: 0.3841 time to fit residues: 61.4746 Evaluate side-chains 64 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 684 HIS 1 739 GLN ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS C 372 ASN C 450 ASN C 495 HIS A Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.038874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.031903 restraints weight = 583972.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.032482 restraints weight = 363520.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.032584 restraints weight = 247385.267| |-----------------------------------------------------------------------------| r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2368 r_free = 0.2368 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2367 r_free = 0.2367 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17405 Z= 0.207 Angle : 0.617 9.238 23638 Z= 0.319 Chirality : 0.042 0.153 2626 Planarity : 0.004 0.038 2972 Dihedral : 8.197 73.166 2483 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2006 helix: 1.61 (0.16), residues: 935 sheet: 0.16 (0.32), residues: 232 loop : 0.54 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 31 HIS 0.013 0.002 HIS 1 407 PHE 0.022 0.002 PHE B 75 TYR 0.029 0.002 TYR B 128 ARG 0.014 0.001 ARG 1 677 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 835) hydrogen bonds : angle 5.27459 ( 2356) metal coordination : bond 0.00559 ( 4) metal coordination : angle 4.46255 ( 12) covalent geometry : bond 0.00437 (17401) covalent geometry : angle 0.60922 (23626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 430 MET cc_start: 0.6332 (mmm) cc_final: 0.6124 (mmm) REVERT: 1 719 MET cc_start: 0.8816 (mtp) cc_final: 0.8433 (mmm) REVERT: 1 863 MET cc_start: 0.8200 (mmp) cc_final: 0.7972 (mmp) REVERT: 1 1001 MET cc_start: 0.9467 (mtm) cc_final: 0.9186 (mtp) REVERT: 1 1376 MET cc_start: 0.9347 (mmt) cc_final: 0.9062 (mmp) REVERT: A 42 MET cc_start: 0.9214 (mmm) cc_final: 0.8969 (mmm) REVERT: A 141 MET cc_start: 0.8708 (mtm) cc_final: 0.8470 (mtm) REVERT: A 184 ARG cc_start: 0.8832 (mtt-85) cc_final: 0.8039 (mtp85) REVERT: A 228 MET cc_start: 0.8701 (mmm) cc_final: 0.8497 (mmm) REVERT: B 162 MET cc_start: 0.9441 (mtp) cc_final: 0.9182 (mtm) REVERT: C 431 MET cc_start: 0.8494 (mtp) cc_final: 0.8288 (mtp) REVERT: C 518 MET cc_start: 0.9551 (mmp) cc_final: 0.9269 (mmp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.4492 time to fit residues: 49.5964 Evaluate side-chains 61 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 180 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 195 optimal weight: 30.0000 chunk 193 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 353 GLN ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 679 ASN ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.038038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.031428 restraints weight = 476144.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.031884 restraints weight = 315550.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.031871 restraints weight = 266876.816| |-----------------------------------------------------------------------------| r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2348 r_free = 0.2348 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2348 r_free = 0.2348 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17405 Z= 0.156 Angle : 0.531 8.951 23638 Z= 0.270 Chirality : 0.040 0.142 2626 Planarity : 0.004 0.049 2972 Dihedral : 7.998 73.272 2483 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 2006 helix: 2.11 (0.17), residues: 934 sheet: 0.54 (0.32), residues: 240 loop : 0.72 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 671 HIS 0.015 0.001 HIS 1 407 PHE 0.017 0.002 PHE B 75 TYR 0.020 0.001 TYR B 128 ARG 0.009 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 835) hydrogen bonds : angle 4.81885 ( 2356) metal coordination : bond 0.00622 ( 4) metal coordination : angle 5.33012 ( 12) covalent geometry : bond 0.00337 (17401) covalent geometry : angle 0.51754 (23626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8767 (tpp) cc_final: 0.8035 (tpp) REVERT: 1 719 MET cc_start: 0.8694 (mtp) cc_final: 0.8295 (mmm) REVERT: A 141 MET cc_start: 0.8629 (mtm) cc_final: 0.8285 (mtm) REVERT: A 184 ARG cc_start: 0.9008 (mtt-85) cc_final: 0.8234 (mtt-85) REVERT: B 162 MET cc_start: 0.9442 (mtp) cc_final: 0.9209 (ptp) REVERT: C 518 MET cc_start: 0.9425 (mmp) cc_final: 0.9097 (mmp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3520 time to fit residues: 37.0417 Evaluate side-chains 56 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 21 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.037331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2319 r_free = 0.2319 target = 0.030886 restraints weight = 545314.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.031485 restraints weight = 348530.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2339 r_free = 0.2339 target = 0.031473 restraints weight = 269764.154| |-----------------------------------------------------------------------------| r_work (final): 0.2333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2333 r_free = 0.2333 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2333 r_free = 0.2333 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17405 Z= 0.184 Angle : 0.543 9.064 23638 Z= 0.272 Chirality : 0.040 0.136 2626 Planarity : 0.004 0.053 2972 Dihedral : 8.007 73.322 2483 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 2006 helix: 2.19 (0.17), residues: 937 sheet: 0.38 (0.32), residues: 229 loop : 0.79 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 856 PHE 0.017 0.001 PHE B 75 TYR 0.023 0.001 TYR 11386 ARG 0.011 0.001 ARG 11276 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 835) hydrogen bonds : angle 4.81028 ( 2356) metal coordination : bond 0.00717 ( 4) metal coordination : angle 5.64963 ( 12) covalent geometry : bond 0.00390 (17401) covalent geometry : angle 0.52846 (23626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.9159 (ttm) cc_final: 0.8777 (tpp) REVERT: 1 719 MET cc_start: 0.8710 (mtp) cc_final: 0.8298 (mmm) REVERT: 1 919 GLU cc_start: 0.9734 (mt-10) cc_final: 0.9500 (mt-10) REVERT: A 114 MET cc_start: 0.8892 (tpp) cc_final: 0.8598 (tpp) REVERT: A 141 MET cc_start: 0.8632 (mtm) cc_final: 0.8203 (mtm) REVERT: A 319 LYS cc_start: 0.6354 (mttm) cc_final: 0.6137 (mttp) REVERT: C 518 MET cc_start: 0.9409 (mmp) cc_final: 0.9067 (mmp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3595 time to fit residues: 37.7440 Evaluate side-chains 59 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 184 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 86 optimal weight: 40.0000 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.037654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.031168 restraints weight = 555417.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.031613 restraints weight = 357047.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.031707 restraints weight = 258849.689| |-----------------------------------------------------------------------------| r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17405 Z= 0.119 Angle : 0.497 10.145 23638 Z= 0.247 Chirality : 0.039 0.135 2626 Planarity : 0.003 0.054 2972 Dihedral : 7.925 73.368 2483 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.19), residues: 2006 helix: 2.30 (0.17), residues: 942 sheet: 0.44 (0.30), residues: 247 loop : 0.81 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.004 0.001 HIS C 692 PHE 0.016 0.001 PHE B 75 TYR 0.015 0.001 TYR B 128 ARG 0.011 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 835) hydrogen bonds : angle 4.65140 ( 2356) metal coordination : bond 0.00581 ( 4) metal coordination : angle 6.02494 ( 12) covalent geometry : bond 0.00257 (17401) covalent geometry : angle 0.47866 (23626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 2.477 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8983 (ttm) cc_final: 0.8759 (tpp) REVERT: 1 719 MET cc_start: 0.8705 (mtp) cc_final: 0.8257 (mmm) REVERT: 1 919 GLU cc_start: 0.9724 (mt-10) cc_final: 0.9476 (mt-10) REVERT: 1 1376 MET cc_start: 0.7947 (mmp) cc_final: 0.6876 (mmm) REVERT: A 114 MET cc_start: 0.8944 (tpp) cc_final: 0.8667 (tpp) REVERT: A 141 MET cc_start: 0.8583 (mtm) cc_final: 0.8203 (mtm) REVERT: A 184 ARG cc_start: 0.9027 (mtt-85) cc_final: 0.8201 (mtt-85) REVERT: B 380 PHE cc_start: 0.7482 (m-10) cc_final: 0.6968 (m-80) REVERT: C 518 MET cc_start: 0.9360 (mmp) cc_final: 0.9025 (mmp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.4471 time to fit residues: 48.9874 Evaluate side-chains 54 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 4 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 168 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 63 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 overall best weight: 6.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.036589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2306 r_free = 0.2306 target = 0.030067 restraints weight = 596562.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2309 r_free = 0.2309 target = 0.030486 restraints weight = 381861.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2320 r_free = 0.2320 target = 0.030679 restraints weight = 274570.903| |-----------------------------------------------------------------------------| r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2314 r_free = 0.2314 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2314 r_free = 0.2314 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17405 Z= 0.206 Angle : 0.568 10.185 23638 Z= 0.282 Chirality : 0.040 0.136 2626 Planarity : 0.004 0.055 2972 Dihedral : 8.042 73.325 2483 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2006 helix: 2.10 (0.17), residues: 955 sheet: 0.18 (0.32), residues: 232 loop : 0.72 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 1 671 HIS 0.010 0.001 HIS B 131 PHE 0.056 0.002 PHE B 132 TYR 0.017 0.002 TYR B 503 ARG 0.006 0.001 ARG 11276 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 835) hydrogen bonds : angle 4.79494 ( 2356) metal coordination : bond 0.00928 ( 4) metal coordination : angle 6.23632 ( 12) covalent geometry : bond 0.00435 (17401) covalent geometry : angle 0.55058 (23626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.9098 (ttm) cc_final: 0.8855 (tpp) REVERT: 1 719 MET cc_start: 0.8715 (mtp) cc_final: 0.8254 (mmm) REVERT: 1 1001 MET cc_start: 0.8966 (ttt) cc_final: 0.8748 (tpp) REVERT: A 42 MET cc_start: 0.9326 (mmm) cc_final: 0.8929 (mmm) REVERT: A 141 MET cc_start: 0.8672 (mtm) cc_final: 0.8198 (mtm) REVERT: A 319 LYS cc_start: 0.6344 (mttm) cc_final: 0.6141 (mttm) REVERT: B 380 PHE cc_start: 0.7587 (m-10) cc_final: 0.7166 (m-80) REVERT: C 518 MET cc_start: 0.9352 (mmp) cc_final: 0.9093 (mmp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.4109 time to fit residues: 39.5188 Evaluate side-chains 55 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 171 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 137 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 44 optimal weight: 40.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 808 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.036131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2302 r_free = 0.2302 target = 0.029667 restraints weight = 650781.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2292 r_free = 0.2292 target = 0.029951 restraints weight = 409062.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2303 r_free = 0.2303 target = 0.030143 restraints weight = 282352.997| |-----------------------------------------------------------------------------| r_work (final): 0.2295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2295 r_free = 0.2295 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2295 r_free = 0.2295 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17405 Z= 0.233 Angle : 0.603 11.163 23638 Z= 0.297 Chirality : 0.040 0.133 2626 Planarity : 0.004 0.071 2972 Dihedral : 8.126 73.318 2483 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2006 helix: 2.00 (0.17), residues: 951 sheet: 0.04 (0.31), residues: 236 loop : 0.69 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 1 671 HIS 0.010 0.001 HIS A 34 PHE 0.033 0.002 PHE B 132 TYR 0.018 0.002 TYR B 503 ARG 0.015 0.001 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 835) hydrogen bonds : angle 4.90586 ( 2356) metal coordination : bond 0.00857 ( 4) metal coordination : angle 7.02336 ( 12) covalent geometry : bond 0.00493 (17401) covalent geometry : angle 0.58184 (23626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 2.007 Fit side-chains revert: symmetry clash REVERT: 1 719 MET cc_start: 0.8689 (mtp) cc_final: 0.8243 (mmm) REVERT: 1 1059 ASN cc_start: 0.9629 (t0) cc_final: 0.9418 (t0) REVERT: A 42 MET cc_start: 0.9322 (mmm) cc_final: 0.8961 (mmm) REVERT: A 184 ARG cc_start: 0.9060 (mtt-85) cc_final: 0.8240 (mtt-85) REVERT: B 380 PHE cc_start: 0.7635 (m-10) cc_final: 0.7279 (m-80) REVERT: C 518 MET cc_start: 0.9332 (mmp) cc_final: 0.9098 (mmp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.4080 time to fit residues: 37.1848 Evaluate side-chains 52 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 64 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 195 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 712 GLN 11036 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.036036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2306 r_free = 0.2306 target = 0.029765 restraints weight = 480733.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2317 r_free = 0.2317 target = 0.030227 restraints weight = 325936.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2308 r_free = 0.2308 target = 0.030150 restraints weight = 268902.212| |-----------------------------------------------------------------------------| r_work (final): 0.2300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2300 r_free = 0.2300 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2300 r_free = 0.2300 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17405 Z= 0.207 Angle : 0.582 11.690 23638 Z= 0.286 Chirality : 0.040 0.133 2626 Planarity : 0.004 0.058 2972 Dihedral : 8.130 73.403 2483 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 2006 helix: 1.94 (0.17), residues: 956 sheet: 0.09 (0.32), residues: 233 loop : 0.64 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 1 671 HIS 0.007 0.001 HIS A 34 PHE 0.027 0.002 PHE B 132 TYR 0.017 0.001 TYR B 503 ARG 0.005 0.001 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 835) hydrogen bonds : angle 4.90099 ( 2356) metal coordination : bond 0.00836 ( 4) metal coordination : angle 7.42032 ( 12) covalent geometry : bond 0.00438 (17401) covalent geometry : angle 0.55776 (23626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 533 MET cc_start: 0.8231 (ptp) cc_final: 0.7929 (ptp) REVERT: 1 719 MET cc_start: 0.8605 (mtp) cc_final: 0.8190 (mmm) REVERT: 1 863 MET cc_start: 0.8392 (mmp) cc_final: 0.7965 (mmm) REVERT: A 42 MET cc_start: 0.9385 (mmm) cc_final: 0.9124 (mmm) REVERT: A 184 ARG cc_start: 0.9071 (mtt-85) cc_final: 0.8233 (mtt-85) REVERT: B 480 MET cc_start: 0.7628 (ttp) cc_final: 0.6768 (mmm) REVERT: C 518 MET cc_start: 0.9322 (mmp) cc_final: 0.8974 (mmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3852 time to fit residues: 34.7233 Evaluate side-chains 52 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 93 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.035815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2282 r_free = 0.2282 target = 0.029518 restraints weight = 507808.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.029900 restraints weight = 336487.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2299 r_free = 0.2299 target = 0.030006 restraints weight = 266669.951| |-----------------------------------------------------------------------------| r_work (final): 0.2294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2294 r_free = 0.2294 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2294 r_free = 0.2294 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17405 Z= 0.230 Angle : 0.602 12.116 23638 Z= 0.297 Chirality : 0.040 0.135 2626 Planarity : 0.004 0.058 2972 Dihedral : 8.164 73.414 2483 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.19), residues: 2006 helix: 1.87 (0.16), residues: 956 sheet: 0.17 (0.33), residues: 228 loop : 0.58 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 1 671 HIS 0.005 0.001 HIS C 639 PHE 0.027 0.002 PHE B 132 TYR 0.018 0.001 TYR B 503 ARG 0.005 0.001 ARG 11276 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 835) hydrogen bonds : angle 4.96137 ( 2356) metal coordination : bond 0.00896 ( 4) metal coordination : angle 7.56693 ( 12) covalent geometry : bond 0.00483 (17401) covalent geometry : angle 0.57766 (23626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 2.077 Fit side-chains REVERT: 1 533 MET cc_start: 0.8269 (ptp) cc_final: 0.7970 (ptp) REVERT: 1 719 MET cc_start: 0.8608 (mtp) cc_final: 0.8172 (mmm) REVERT: 1 1376 MET cc_start: 0.8163 (mmp) cc_final: 0.7942 (mmp) REVERT: A 42 MET cc_start: 0.9385 (mmm) cc_final: 0.9127 (mmm) REVERT: A 184 ARG cc_start: 0.9033 (mtt-85) cc_final: 0.8223 (mtt-85) REVERT: B 480 MET cc_start: 0.7669 (ttp) cc_final: 0.6774 (mmm) REVERT: C 518 MET cc_start: 0.9310 (mmp) cc_final: 0.8989 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3070 time to fit residues: 28.1816 Evaluate side-chains 50 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 168 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 173 optimal weight: 0.3980 chunk 85 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 184 optimal weight: 0.0770 chunk 95 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.036717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2333 r_free = 0.2333 target = 0.030291 restraints weight = 545957.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.030566 restraints weight = 357642.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.030706 restraints weight = 267488.733| |-----------------------------------------------------------------------------| r_work (final): 0.2329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2329 r_free = 0.2329 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2329 r_free = 0.2329 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17405 Z= 0.112 Angle : 0.536 11.471 23638 Z= 0.261 Chirality : 0.040 0.178 2626 Planarity : 0.004 0.057 2972 Dihedral : 8.020 73.503 2483 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2006 helix: 2.05 (0.17), residues: 956 sheet: 0.34 (0.34), residues: 216 loop : 0.73 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.006 0.001 HIS B 131 PHE 0.021 0.001 PHE B 132 TYR 0.015 0.001 TYR 1 472 ARG 0.004 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 835) hydrogen bonds : angle 4.75538 ( 2356) metal coordination : bond 0.00715 ( 4) metal coordination : angle 7.67112 ( 12) covalent geometry : bond 0.00241 (17401) covalent geometry : angle 0.50715 (23626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.816 Fit side-chains REVERT: 1 354 MET cc_start: 0.8653 (tpp) cc_final: 0.8429 (tpt) REVERT: 1 719 MET cc_start: 0.8543 (mtp) cc_final: 0.8126 (mmm) REVERT: 1 863 MET cc_start: 0.8335 (mmp) cc_final: 0.8099 (mmm) REVERT: A 42 MET cc_start: 0.9404 (mmm) cc_final: 0.9072 (mmm) REVERT: A 184 ARG cc_start: 0.9079 (mtt-85) cc_final: 0.8248 (mtt-85) REVERT: B 380 PHE cc_start: 0.7648 (m-10) cc_final: 0.7358 (m-80) REVERT: B 480 MET cc_start: 0.7495 (ttp) cc_final: 0.6592 (mmm) REVERT: C 518 MET cc_start: 0.9292 (mmp) cc_final: 0.8989 (mmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2996 time to fit residues: 28.2929 Evaluate side-chains 51 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 86 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.035984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2284 r_free = 0.2284 target = 0.029541 restraints weight = 559368.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.029887 restraints weight = 351283.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2298 r_free = 0.2298 target = 0.029980 restraints weight = 278003.158| |-----------------------------------------------------------------------------| r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2293 r_free = 0.2293 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2293 r_free = 0.2293 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17405 Z= 0.208 Angle : 0.589 12.139 23638 Z= 0.290 Chirality : 0.040 0.165 2626 Planarity : 0.004 0.057 2972 Dihedral : 8.079 73.432 2483 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 2006 helix: 1.94 (0.17), residues: 963 sheet: 0.05 (0.33), residues: 239 loop : 0.72 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 1 671 HIS 0.005 0.001 HIS B 131 PHE 0.023 0.002 PHE B 132 TYR 0.017 0.001 TYR B 503 ARG 0.005 0.001 ARG 11276 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 835) hydrogen bonds : angle 4.87349 ( 2356) metal coordination : bond 0.00888 ( 4) metal coordination : angle 7.38729 ( 12) covalent geometry : bond 0.00441 (17401) covalent geometry : angle 0.56476 (23626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6240.63 seconds wall clock time: 114 minutes 46.48 seconds (6886.48 seconds total)