Starting phenix.real_space_refine on Sun Aug 24 04:38:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8foh_29349/08_2025/8foh_29349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foh_29349/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2025/8foh_29349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2025/8foh_29349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2025/8foh_29349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2025/8foh_29349.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP: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: {'ARG:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP: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, 'ARG:plan': 1, 'GLN:plan1': 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, 'ARG:plan': 2, 'TYR: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, 'ARG:plan': 2, 'TYR: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: 6.64, per 1000 atoms: 0.39 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: 1.62 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.66 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: 3.25 Time building geometry restraints manager: 2.10 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: 1.160 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.002 ARG A 45 TYR 0.250 0.011 TYR B 55 PHE 0.065 0.007 PHE B 138 TRP 0.056 0.010 TRP B 78 HIS 0.031 0.005 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.01290 (17401) covalent geometry : angle 1.46230 (23626) hydrogen bonds : bond 0.16423 ( 835) hydrogen bonds : angle 7.21691 ( 2356) metal coordination : bond 0.02834 ( 4) metal coordination : angle 5.04449 ( 12) *********************** 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 : 0.726 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: 0.9078 (mmm) REVERT: 1 1438 MET cc_start: 0.8997 (mmp) cc_final: 0.8783 (mmm) REVERT: A 108 LEU cc_start: 0.9003 (tp) cc_final: 0.8786 (mt) REVERT: A 141 MET cc_start: 0.8933 (mtm) cc_final: 0.8727 (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: 0.1842 time to fit residues: 28.6214 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 : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.2690 r_free = 0.2690 target = 0.039169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.032187 restraints weight = 615581.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.032833 restraints weight = 370216.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.032945 restraints weight = 236106.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.033106 restraints weight = 199513.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.033254 restraints weight = 185388.023| |-----------------------------------------------------------------------------| r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2398 r_free = 0.2398 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17405 Z= 0.189 Angle : 0.606 9.275 23638 Z= 0.313 Chirality : 0.042 0.138 2626 Planarity : 0.004 0.044 2972 Dihedral : 8.185 73.161 2483 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.18), residues: 2006 helix: 1.61 (0.16), residues: 941 sheet: 0.19 (0.33), residues: 227 loop : 0.51 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 286 TYR 0.029 0.002 TYR B 128 PHE 0.021 0.002 PHE B 75 TRP 0.015 0.002 TRP A 31 HIS 0.013 0.002 HIS 1 407 Details of bonding type rmsd covalent geometry : bond 0.00398 (17401) covalent geometry : angle 0.59770 (23626) hydrogen bonds : bond 0.04377 ( 835) hydrogen bonds : angle 5.25891 ( 2356) metal coordination : bond 0.00633 ( 4) metal coordination : angle 4.35213 ( 12) *********************** 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 74 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 430 MET cc_start: 0.6316 (mmm) cc_final: 0.6096 (mmm) REVERT: 1 533 MET cc_start: 0.8180 (ptp) cc_final: 0.7780 (ttp) REVERT: 1 719 MET cc_start: 0.8839 (mtp) cc_final: 0.8458 (mmm) REVERT: 1 863 MET cc_start: 0.8207 (mmp) cc_final: 0.7972 (mmp) REVERT: 1 1001 MET cc_start: 0.9499 (mtm) cc_final: 0.9196 (mtp) REVERT: 1 1376 MET cc_start: 0.9317 (mmt) cc_final: 0.9026 (mmp) REVERT: A 42 MET cc_start: 0.9202 (mmm) cc_final: 0.8966 (mmm) REVERT: A 141 MET cc_start: 0.8741 (mtm) cc_final: 0.8527 (mtm) REVERT: A 228 MET cc_start: 0.8704 (mmm) cc_final: 0.8480 (mmm) REVERT: B 162 MET cc_start: 0.9414 (mtp) cc_final: 0.9149 (mtm) REVERT: C 518 MET cc_start: 0.9575 (mmp) cc_final: 0.9300 (mmp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1391 time to fit residues: 16.0031 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 33 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** 1 769 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 = 0.2645 r_free = 0.2645 target = 0.037909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.031253 restraints weight = 469807.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.031531 restraints weight = 312583.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.031565 restraints weight = 265447.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.031902 restraints weight = 217561.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.031941 restraints weight = 195621.403| |-----------------------------------------------------------------------------| r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2357 r_free = 0.2357 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2357 r_free = 0.2357 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17405 Z= 0.175 Angle : 0.552 8.646 23638 Z= 0.280 Chirality : 0.041 0.291 2626 Planarity : 0.004 0.050 2972 Dihedral : 8.031 73.208 2483 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.80 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.19), residues: 2006 helix: 2.03 (0.17), residues: 941 sheet: 0.51 (0.32), residues: 238 loop : 0.69 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 677 TYR 0.018 0.001 TYR B 128 PHE 0.019 0.002 PHE B 75 TRP 0.015 0.002 TRP 1 671 HIS 0.015 0.001 HIS 1 407 Details of bonding type rmsd covalent geometry : bond 0.00373 (17401) covalent geometry : angle 0.53924 (23626) hydrogen bonds : bond 0.03656 ( 835) hydrogen bonds : angle 4.87672 ( 2356) metal coordination : bond 0.00707 ( 4) metal coordination : angle 5.25173 ( 12) *********************** 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 66 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8668 (tpp) cc_final: 0.8300 (tpp) REVERT: 1 430 MET cc_start: 0.6574 (mmm) cc_final: 0.6367 (mmm) REVERT: 1 719 MET cc_start: 0.8676 (mtp) cc_final: 0.8374 (mmm) REVERT: 1 1376 MET cc_start: 0.9390 (mmt) cc_final: 0.8538 (mmm) REVERT: A 141 MET cc_start: 0.8610 (mtm) cc_final: 0.8280 (mtm) REVERT: A 184 ARG cc_start: 0.8971 (mtt-85) cc_final: 0.8218 (mtt-85) REVERT: B 162 MET cc_start: 0.9433 (mtp) cc_final: 0.9204 (ptp) REVERT: C 518 MET cc_start: 0.9422 (mmp) cc_final: 0.9096 (mmp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1479 time to fit residues: 15.1762 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 : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 200 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 195 optimal weight: 30.0000 chunk 57 optimal weight: 9.9990 chunk 146 optimal weight: 0.0470 chunk 45 optimal weight: 9.9990 chunk 63 optimal weight: 0.0060 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 overall best weight: 3.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.037982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.031030 restraints weight = 595738.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.031945 restraints weight = 389897.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.032079 restraints weight = 211628.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.032384 restraints weight = 187323.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.032420 restraints weight = 179947.757| |-----------------------------------------------------------------------------| r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17405 Z= 0.121 Angle : 0.501 9.557 23638 Z= 0.249 Chirality : 0.039 0.135 2626 Planarity : 0.003 0.053 2972 Dihedral : 7.924 73.368 2483 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.19), residues: 2006 helix: 2.23 (0.17), residues: 941 sheet: 0.54 (0.31), residues: 245 loop : 0.83 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 11276 TYR 0.025 0.001 TYR 11386 PHE 0.017 0.001 PHE B 75 TRP 0.009 0.001 TRP 1 671 HIS 0.004 0.001 HIS C 639 Details of bonding type rmsd covalent geometry : bond 0.00262 (17401) covalent geometry : angle 0.48508 (23626) hydrogen bonds : bond 0.03208 ( 835) hydrogen bonds : angle 4.70365 ( 2356) metal coordination : bond 0.00609 ( 4) metal coordination : angle 5.53065 ( 12) *********************** 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 67 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: 1 719 MET cc_start: 0.8669 (mtp) cc_final: 0.8360 (mmm) REVERT: 1 919 GLU cc_start: 0.9717 (mt-10) cc_final: 0.9467 (mt-10) REVERT: 1 1376 MET cc_start: 0.9392 (mmt) cc_final: 0.8468 (mmm) REVERT: A 141 MET cc_start: 0.8552 (mtm) cc_final: 0.8121 (mtm) REVERT: A 184 ARG cc_start: 0.8992 (mtt-85) cc_final: 0.8151 (mtp85) REVERT: B 162 MET cc_start: 0.9411 (mtp) cc_final: 0.9182 (ptp) REVERT: B 480 MET cc_start: 0.7366 (ttp) cc_final: 0.7158 (ttp) REVERT: C 518 MET cc_start: 0.9369 (mmp) cc_final: 0.9046 (mmp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1288 time to fit residues: 13.5019 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 : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 63 optimal weight: 40.0000 chunk 22 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 638 HIS 1 679 ASN ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.037611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.031018 restraints weight = 541916.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.031631 restraints weight = 346950.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.031690 restraints weight = 254911.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.031768 restraints weight = 205157.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.031988 restraints weight = 188102.474| |-----------------------------------------------------------------------------| r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2370 r_free = 0.2370 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2370 r_free = 0.2370 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17405 Z= 0.140 Angle : 0.509 9.347 23638 Z= 0.253 Chirality : 0.039 0.134 2626 Planarity : 0.003 0.054 2972 Dihedral : 7.914 73.316 2483 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.19), residues: 2006 helix: 2.26 (0.17), residues: 950 sheet: 0.57 (0.31), residues: 247 loop : 0.81 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 11276 TYR 0.016 0.001 TYR B 128 PHE 0.017 0.001 PHE B 75 TRP 0.012 0.001 TRP 1 671 HIS 0.004 0.001 HIS C 639 Details of bonding type rmsd covalent geometry : bond 0.00300 (17401) covalent geometry : angle 0.49300 (23626) hydrogen bonds : bond 0.03136 ( 835) hydrogen bonds : angle 4.66647 ( 2356) metal coordination : bond 0.00619 ( 4) metal coordination : angle 5.69893 ( 12) *********************** 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 67 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: 1 719 MET cc_start: 0.8649 (mtp) cc_final: 0.8323 (mmm) REVERT: 1 919 GLU cc_start: 0.9719 (mt-10) cc_final: 0.9458 (mt-10) REVERT: 1 1376 MET cc_start: 0.9408 (mmt) cc_final: 0.8339 (mmm) REVERT: A 141 MET cc_start: 0.8591 (mtm) cc_final: 0.8216 (mtm) REVERT: A 184 ARG cc_start: 0.8997 (mtt-85) cc_final: 0.8206 (mtp85) REVERT: A 319 LYS cc_start: 0.6282 (mttm) cc_final: 0.6014 (mttm) REVERT: C 518 MET cc_start: 0.9365 (mmp) cc_final: 0.9021 (mmp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1541 time to fit residues: 16.0845 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 : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 173 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11036 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.037601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.030909 restraints weight = 620755.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.031462 restraints weight = 371538.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.031614 restraints weight = 261572.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.031685 restraints weight = 210486.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.031885 restraints weight = 193908.845| |-----------------------------------------------------------------------------| r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2370 r_free = 0.2370 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2370 r_free = 0.2370 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17405 Z= 0.124 Angle : 0.491 9.696 23638 Z= 0.244 Chirality : 0.039 0.137 2626 Planarity : 0.003 0.054 2972 Dihedral : 7.874 73.348 2483 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 2006 helix: 2.34 (0.17), residues: 950 sheet: 0.43 (0.31), residues: 235 loop : 0.84 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 267 TYR 0.014 0.001 TYR B 503 PHE 0.054 0.001 PHE B 132 TRP 0.010 0.001 TRP 1 671 HIS 0.007 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00269 (17401) covalent geometry : angle 0.47241 (23626) hydrogen bonds : bond 0.02993 ( 835) hydrogen bonds : angle 4.60360 ( 2356) metal coordination : bond 0.00562 ( 4) metal coordination : angle 5.89089 ( 12) *********************** 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 64 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 383 MET cc_start: 0.8793 (tmm) cc_final: 0.7736 (tmm) REVERT: 1 719 MET cc_start: 0.8702 (mtp) cc_final: 0.8362 (mmm) REVERT: 1 919 GLU cc_start: 0.9715 (mt-10) cc_final: 0.9448 (mt-10) REVERT: 1 1376 MET cc_start: 0.9396 (mmt) cc_final: 0.9112 (tpp) REVERT: A 42 MET cc_start: 0.9228 (mmm) cc_final: 0.8845 (mmm) REVERT: A 141 MET cc_start: 0.8559 (mtm) cc_final: 0.8094 (mtm) REVERT: A 184 ARG cc_start: 0.8977 (mtt-85) cc_final: 0.8263 (mtt-85) REVERT: A 319 LYS cc_start: 0.6283 (mttm) cc_final: 0.5944 (mttm) REVERT: B 56 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8665 (mp0) REVERT: B 380 PHE cc_start: 0.7463 (m-10) cc_final: 0.6964 (m-80) REVERT: C 518 MET cc_start: 0.9346 (mmp) cc_final: 0.9075 (mmp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1403 time to fit residues: 14.3034 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 : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 15 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 43 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 808 ASN 11369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.037468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2339 r_free = 0.2339 target = 0.030913 restraints weight = 515729.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.031498 restraints weight = 328734.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.031530 restraints weight = 248861.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.031606 restraints weight = 201783.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.031780 restraints weight = 187066.910| |-----------------------------------------------------------------------------| r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2370 r_free = 0.2370 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 = 0.2370 r_free = 0.2370 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17405 Z= 0.127 Angle : 0.497 9.257 23638 Z= 0.246 Chirality : 0.039 0.138 2626 Planarity : 0.003 0.055 2972 Dihedral : 7.851 73.333 2483 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.19), residues: 2006 helix: 2.41 (0.17), residues: 951 sheet: 0.50 (0.32), residues: 237 loop : 0.84 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 177 TYR 0.014 0.001 TYR B 503 PHE 0.029 0.001 PHE B 132 TRP 0.012 0.001 TRP 1 671 HIS 0.010 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00275 (17401) covalent geometry : angle 0.47842 (23626) hydrogen bonds : bond 0.02943 ( 835) hydrogen bonds : angle 4.58797 ( 2356) metal coordination : bond 0.00593 ( 4) metal coordination : angle 5.93302 ( 12) *********************** 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 63 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 383 MET cc_start: 0.8871 (tmm) cc_final: 0.7759 (tmm) REVERT: 1 719 MET cc_start: 0.8691 (mtp) cc_final: 0.8216 (mmm) REVERT: 1 1059 ASN cc_start: 0.9546 (t0) cc_final: 0.9296 (t0) REVERT: 1 1376 MET cc_start: 0.9431 (mmt) cc_final: 0.9146 (tpp) REVERT: A 42 MET cc_start: 0.9310 (mmm) cc_final: 0.8959 (mmm) REVERT: A 141 MET cc_start: 0.8593 (mtm) cc_final: 0.8231 (mtm) REVERT: A 184 ARG cc_start: 0.8998 (mtt-85) cc_final: 0.8261 (mtp85) REVERT: A 319 LYS cc_start: 0.6369 (mttm) cc_final: 0.5888 (mttp) REVERT: C 518 MET cc_start: 0.9341 (mmp) cc_final: 0.9082 (mmp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1448 time to fit residues: 14.4214 Evaluate side-chains 53 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 154 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 712 GLN ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.036402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.029945 restraints weight = 528418.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.030430 restraints weight = 351526.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.030540 restraints weight = 257476.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.030609 restraints weight = 210829.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2333 r_free = 0.2333 target = 0.030744 restraints weight = 193127.732| |-----------------------------------------------------------------------------| r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2328 r_free = 0.2328 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 = 0.2328 r_free = 0.2328 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17405 Z= 0.207 Angle : 0.573 10.503 23638 Z= 0.285 Chirality : 0.040 0.135 2626 Planarity : 0.004 0.056 2972 Dihedral : 8.000 73.375 2483 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.19), residues: 2006 helix: 2.18 (0.17), residues: 952 sheet: 0.29 (0.32), residues: 238 loop : 0.76 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 177 TYR 0.018 0.001 TYR B 503 PHE 0.032 0.002 PHE B 132 TRP 0.018 0.002 TRP 1 671 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00437 (17401) covalent geometry : angle 0.55488 (23626) hydrogen bonds : bond 0.03298 ( 835) hydrogen bonds : angle 4.80470 ( 2356) metal coordination : bond 0.00941 ( 4) metal coordination : angle 6.41251 ( 12) *********************** 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 : 0.732 Fit side-chains revert: symmetry clash REVERT: 1 719 MET cc_start: 0.8688 (mtp) cc_final: 0.8167 (mmm) REVERT: 1 863 MET cc_start: 0.8178 (mmp) cc_final: 0.7919 (mmm) REVERT: 1 1059 ASN cc_start: 0.9648 (t0) cc_final: 0.9414 (t0) REVERT: 1 1376 MET cc_start: 0.9500 (mmt) cc_final: 0.8501 (mmm) REVERT: A 42 MET cc_start: 0.9342 (mmm) cc_final: 0.9021 (mmm) REVERT: A 141 MET cc_start: 0.8690 (mtm) cc_final: 0.8230 (mtm) REVERT: A 184 ARG cc_start: 0.8971 (mtt-85) cc_final: 0.8253 (mtp85) REVERT: A 319 LYS cc_start: 0.6382 (mttm) cc_final: 0.5923 (mttp) REVERT: B 380 PHE cc_start: 0.7494 (m-10) cc_final: 0.7128 (m-80) REVERT: C 518 MET cc_start: 0.9342 (mmp) cc_final: 0.9103 (mmp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1401 time to fit residues: 12.9359 Evaluate side-chains 53 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 95 optimal weight: 0.0170 chunk 121 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 0.0980 overall best weight: 2.6224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2646 r_free = 0.2646 target = 0.037146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.030755 restraints weight = 510639.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.031117 restraints weight = 347724.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.031219 restraints weight = 251413.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.031528 restraints weight = 198511.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.031574 restraints weight = 178805.816| |-----------------------------------------------------------------------------| r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2369 r_free = 0.2369 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 = 0.2369 r_free = 0.2369 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17405 Z= 0.109 Angle : 0.510 10.076 23638 Z= 0.249 Chirality : 0.039 0.139 2626 Planarity : 0.003 0.056 2972 Dihedral : 7.903 73.399 2483 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 2006 helix: 2.33 (0.17), residues: 950 sheet: 0.34 (0.32), residues: 237 loop : 0.89 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.015 0.001 TYR B 503 PHE 0.024 0.001 PHE B 132 TRP 0.008 0.001 TRP 1 671 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00238 (17401) covalent geometry : angle 0.48683 (23626) hydrogen bonds : bond 0.02941 ( 835) hydrogen bonds : angle 4.64688 ( 2356) metal coordination : bond 0.00666 ( 4) metal coordination : angle 6.73915 ( 12) *********************** 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 60 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: 1 619 MET cc_start: 0.8683 (tpp) cc_final: 0.8404 (mmt) REVERT: 1 719 MET cc_start: 0.8666 (mtp) cc_final: 0.8164 (mmm) REVERT: 1 1059 ASN cc_start: 0.9654 (t0) cc_final: 0.9410 (t0) REVERT: 1 1376 MET cc_start: 0.9414 (mmt) cc_final: 0.8399 (mmm) REVERT: 1 1420 GLU cc_start: 0.9061 (tp30) cc_final: 0.8575 (tm-30) REVERT: A 42 MET cc_start: 0.9367 (mmm) cc_final: 0.9125 (mmm) REVERT: A 141 MET cc_start: 0.8620 (mtm) cc_final: 0.8175 (mtm) REVERT: A 184 ARG cc_start: 0.8996 (mtt-85) cc_final: 0.8216 (mtt-85) REVERT: A 319 LYS cc_start: 0.6231 (mttm) cc_final: 0.5835 (mttp) REVERT: B 162 MET cc_start: 0.9375 (ptp) cc_final: 0.9059 (ptp) REVERT: B 380 PHE cc_start: 0.7428 (m-10) cc_final: 0.7064 (m-80) REVERT: B 480 MET cc_start: 0.7454 (ttp) cc_final: 0.6515 (mmm) REVERT: C 518 MET cc_start: 0.9303 (mmp) cc_final: 0.8935 (mmm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1446 time to fit residues: 13.8962 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 : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 55 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.036778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.030043 restraints weight = 604576.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.030637 restraints weight = 353662.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.030669 restraints weight = 280084.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.030828 restraints weight = 225071.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.030950 restraints weight = 204043.273| |-----------------------------------------------------------------------------| r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2344 r_free = 0.2344 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 = 0.2344 r_free = 0.2344 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3884 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= 0.149 Angle : 0.528 10.518 23638 Z= 0.259 Chirality : 0.039 0.140 2626 Planarity : 0.003 0.056 2972 Dihedral : 7.908 73.363 2483 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.19), residues: 2006 helix: 2.29 (0.17), residues: 954 sheet: 0.35 (0.32), residues: 238 loop : 0.92 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 11276 TYR 0.015 0.001 TYR B 503 PHE 0.026 0.001 PHE B 132 TRP 0.014 0.001 TRP 1 671 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00321 (17401) covalent geometry : angle 0.50651 (23626) hydrogen bonds : bond 0.03016 ( 835) hydrogen bonds : angle 4.65703 ( 2356) metal coordination : bond 0.00707 ( 4) metal coordination : angle 6.58170 ( 12) ********************** 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 : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 719 MET cc_start: 0.8659 (mtp) cc_final: 0.8162 (mmm) REVERT: 1 1001 MET cc_start: 0.9024 (tpt) cc_final: 0.8754 (tpp) REVERT: 1 1059 ASN cc_start: 0.9670 (t0) cc_final: 0.9430 (t0) REVERT: 1 1376 MET cc_start: 0.9455 (mmt) cc_final: 0.8446 (mmm) REVERT: A 42 MET cc_start: 0.9408 (mmm) cc_final: 0.9163 (mmm) REVERT: A 141 MET cc_start: 0.8635 (mtm) cc_final: 0.8167 (mtm) REVERT: A 319 LYS cc_start: 0.6173 (mttm) cc_final: 0.5820 (mttp) REVERT: B 162 MET cc_start: 0.9408 (ptp) cc_final: 0.9125 (ptp) REVERT: B 380 PHE cc_start: 0.7530 (m-10) cc_final: 0.7188 (m-80) REVERT: B 480 MET cc_start: 0.7370 (ttp) cc_final: 0.6470 (mmm) REVERT: C 518 MET cc_start: 0.9293 (mmp) cc_final: 0.9073 (mmp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1414 time to fit residues: 13.2258 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 : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 14 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 30 optimal weight: 40.0000 chunk 165 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 185 optimal weight: 0.0980 chunk 50 optimal weight: 0.0170 overall best weight: 6.0228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2620 r_free = 0.2620 target = 0.036389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2299 r_free = 0.2299 target = 0.029789 restraints weight = 601953.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.030254 restraints weight = 359260.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.030394 restraints weight = 271413.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.030512 restraints weight = 220719.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.030647 restraints weight = 200740.613| |-----------------------------------------------------------------------------| r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2330 r_free = 0.2330 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 = 0.2330 r_free = 0.2330 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4066 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= 0.177 Angle : 0.550 11.213 23638 Z= 0.270 Chirality : 0.039 0.135 2626 Planarity : 0.004 0.056 2972 Dihedral : 7.974 73.414 2483 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.19), residues: 2006 helix: 2.15 (0.17), residues: 957 sheet: 0.18 (0.31), residues: 245 loop : 0.84 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 11276 TYR 0.018 0.001 TYR B 503 PHE 0.026 0.001 PHE B 132 TRP 0.016 0.001 TRP 1 671 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00374 (17401) covalent geometry : angle 0.52773 (23626) hydrogen bonds : bond 0.03188 ( 835) hydrogen bonds : angle 4.76177 ( 2356) metal coordination : bond 0.00839 ( 4) metal coordination : angle 6.89787 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2314.26 seconds wall clock time: 41 minutes 15.86 seconds (2475.86 seconds total)