Starting phenix.real_space_refine on Fri Sep 27 20:05:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/09_2024/8foh_29349.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/09_2024/8foh_29349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/09_2024/8foh_29349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/09_2024/8foh_29349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/09_2024/8foh_29349.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/09_2024/8foh_29349.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 20 5.49 5 S 93 5.16 5 C 10746 2.51 5 N 2926 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16996 Number of models: 1 Model: "" Number of chains: 7 Chain: "1" Number of atoms: 7136 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 893, 7128 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 41, 'TRANS': 851} Chain breaks: 12 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 893, 7128 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 41, 'TRANS': 851} Chain breaks: 12 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 7245 Chain: "A" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2780 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 3381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3358 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 406, 3358 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 3402 Chain: "C" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3255 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 5, 'PTRANS': 23, 'TRANS': 381} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 410, 3255 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 5, 'PTRANS': 23, 'TRANS': 381} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3308 Chain: "T" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 241 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "P" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12081 SG CYS B 336 85.739 58.913 110.097 1.00 16.40 S ATOM 12802 SG CYS B 434 84.469 61.343 104.265 1.00 18.69 S ATOM 12670 SG CYS B 417 85.146 54.838 105.091 1.00 17.89 S ATOM 13072 SG CYS B 474 90.063 58.277 105.062 1.00 16.49 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASP 11414 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.50 residue: pdb=" N AASP C 263 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.50 residue: pdb=" N AHIS C 495 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 495 " occ=0.50 Time building chain proxies: 16.09, per 1000 atoms: 0.95 Number of scatterers: 16996 At special positions: 0 Unit cell: (111.78, 119.232, 197.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 93 16.00 P 20 15.00 O 3207 8.00 N 2926 7.00 C 10746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " Number of angles added : 12 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 17 sheets defined 51.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain '1' and resid 402 through 419 Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 480 through 489 Processing helix chain '1' and resid 521 through 525 Processing helix chain '1' and resid 615 through 631 Processing helix chain '1' and resid 643 through 655 Processing helix chain '1' and resid 659 through 664 Processing helix chain '1' and resid 679 through 692 removed outlier: 3.747A pdb=" N HIS 1 684 " --> pdb=" O SER 1 680 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE 1 685 " --> pdb=" O ASN 1 681 " (cutoff:3.500A) Processing helix chain '1' and resid 701 through 707 removed outlier: 3.678A pdb=" N LEU 1 707 " --> pdb=" O MET 1 703 " (cutoff:3.500A) Processing helix chain '1' and resid 715 through 725 Processing helix chain '1' and resid 738 through 743 removed outlier: 4.118A pdb=" N ASN 1 742 " --> pdb=" O PRO 1 738 " (cutoff:3.500A) Processing helix chain '1' and resid 743 through 768 Processing helix chain '1' and resid 769 through 782 Processing helix chain '1' and resid 784 through 791 Processing helix chain '1' and resid 795 through 808 removed outlier: 3.554A pdb=" N TYR 1 799 " --> pdb=" O GLY 1 795 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE 1 800 " --> pdb=" O ARG 1 796 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU 1 801 " --> pdb=" O ASN 1 797 " (cutoff:3.500A) Processing helix chain '1' and resid 867 through 876 removed outlier: 3.608A pdb=" N SER 1 871 " --> pdb=" O SER 1 867 " (cutoff:3.500A) Processing helix chain '1' and resid 906 through 927 removed outlier: 3.711A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 929 through 948 Processing helix chain '1' and resid 950 through 956 removed outlier: 4.163A pdb=" N LEU 1 954 " --> pdb=" O MET 1 950 " (cutoff:3.500A) Processing helix chain '1' and resid 963 through 988 Processing helix chain '1' and resid 1008 through 1027 Processing helix chain '1' and resid 1071 through 1075 Processing helix chain '1' and resid 1080 through 1094 Processing helix chain '1' and resid 1102 through 1119 removed outlier: 3.527A pdb=" N ASP 11112 " --> pdb=" O ASP 11108 " (cutoff:3.500A) Processing helix chain '1' and resid 1211 through 1216 Processing helix chain '1' and resid 1218 through 1226 Processing helix chain '1' and resid 1233 through 1240 Processing helix chain '1' and resid 1322 through 1344 removed outlier: 4.263A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY 11344 " --> pdb=" O LEU 11340 " (cutoff:3.500A) Processing helix chain '1' and resid 1381 through 1396 removed outlier: 3.818A pdb=" N PHE 11396 " --> pdb=" O PHE 11392 " (cutoff:3.500A) Processing helix chain '1' and resid 1397 through 1403 Processing helix chain '1' and resid 1423 through 1434 Processing helix chain '1' and resid 1434 through 1450 removed outlier: 3.608A pdb=" N VAL 11445 " --> pdb=" O GLY 11441 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 114 through 121 removed outlier: 5.101A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 151 removed outlier: 3.645A pdb=" N LYS A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 210 through 229 Proline residue: A 222 - end of helix removed outlier: 4.366A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 269 through 285 removed outlier: 4.061A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.809A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 320' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 74 through 95 Processing helix chain 'B' and resid 98 through 114 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 120 through 139 Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 191 through 208 removed outlier: 4.664A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.575A pdb=" N GLN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.597A pdb=" N ASN B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 282 Proline residue: B 279 - end of helix Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.684A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 334 through 348 Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 368 through 380 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.628A pdb=" N TYR B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 457 through 467 Processing helix chain 'B' and resid 469 through 482 Processing helix chain 'B' and resid 499 through 510 Processing helix chain 'C' and resid 253 through 277 removed outlier: 3.684A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 440 through 446 Processing helix chain 'C' and resid 460 through 469 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 548 through 554 Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 613 through 621 removed outlier: 4.996A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 Processing helix chain 'C' and resid 693 through 697 Processing sheet with id=AA1, first strand: chain '1' and resid 515 through 519 removed outlier: 6.868A pdb=" N SER 1 381 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL 1 517 " --> pdb=" O SER 1 381 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N MET 1 383 " --> pdb=" O VAL 1 517 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL 1 519 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 519 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 1 366 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS 1 371 " --> pdb=" O TRP 1 356 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP 1 356 " --> pdb=" O LYS 1 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 425 through 431 removed outlier: 7.262A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 609 through 612 removed outlier: 6.781A pdb=" N LEU 1 582 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARG 1 611 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR 1 584 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN 1 544 " --> pdb=" O VAL 1 557 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE 1 559 " --> pdb=" O SER 1 542 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER 1 542 " --> pdb=" O ILE 1 559 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU 1 561 " --> pdb=" O SER 1 540 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER 1 540 " --> pdb=" O LEU 1 561 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA 1 563 " --> pdb=" O CYS 1 538 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS 1 538 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG 1 565 " --> pdb=" O LEU 1 536 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU 1 536 " --> pdb=" O ARG 1 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 854 through 856 removed outlier: 6.664A pdb=" N ILE 11034 " --> pdb=" O ASP 1 864 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP 1 864 " --> pdb=" O ILE 11034 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER 1 999 " --> pdb=" O GLY 1 995 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY 1 995 " --> pdb=" O SER 1 999 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET 11001 " --> pdb=" O VAL 1 993 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU 1 991 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 854 through 856 removed outlier: 13.471A pdb=" N ASP 11035 " --> pdb=" O LEU 11056 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N LEU 11056 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL 11037 " --> pdb=" O VAL 11054 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU 11052 " --> pdb=" O LYS 11039 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU 11041 " --> pdb=" O ALA 11050 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA 11050 " --> pdb=" O LEU 11041 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU 11043 " --> pdb=" O LYS 11048 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LYS 11048 " --> pdb=" O LEU 11043 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 1283 through 1286 removed outlier: 4.665A pdb=" N LEU 11283 " --> pdb=" O PHE 11296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 1305 through 1308 Processing sheet with id=AA8, first strand: chain '1' and resid 1356 through 1357 Processing sheet with id=AA9, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.505A pdb=" N TYR A 59 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 47 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 157 through 161 removed outlier: 4.559A pdb=" N ASP A 111 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 181 through 182 removed outlier: 4.071A pdb=" N GLN B 181 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AB4, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB5, first strand: chain 'C' and resid 375 through 376 Processing sheet with id=AB6, first strand: chain 'C' and resid 515 through 517 removed outlier: 6.310A pdb=" N THR C 482 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS C 394 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE C 430 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE C 396 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE C 432 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR C 398 " --> pdb=" O PHE C 432 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.407A pdb=" N TYR C 530 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE C 632 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY C 532 " --> pdb=" O ILE C 632 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 578 through 579 839 hydrogen bonds defined for protein. 2356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.13 Time building geometry restraints manager: 4.76 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: 0.830 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 51.260 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.710 ------------------------------------------------------------------------------- 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 17401 Z= 0.825 Angle : 1.462 13.159 23626 Z= 0.952 Chirality : 0.088 0.699 2626 Planarity : 0.011 0.218 2972 Dihedral : 13.110 87.912 6625 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.61 % Favored : 97.29 % Rotamer: Outliers : 0.49 % Allowed : 3.57 % Favored : 95.94 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2006 helix: -0.26 (0.15), residues: 949 sheet: -0.37 (0.34), residues: 207 loop : -0.03 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.010 TRP B 78 HIS 0.031 0.005 HIS B 348 PHE 0.065 0.007 PHE B 138 TYR 0.250 0.011 TYR B 55 ARG 0.017 0.002 ARG A 45 *********************** 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 fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 652 MET cc_start: 0.8848 (mtt) cc_final: 0.8591 (mtt) REVERT: 1 919 GLU cc_start: 0.9685 (mt-10) cc_final: 0.9442 (mt-10) REVERT: 1 950 MET cc_start: 0.9379 (mmm) cc_final: 0.9077 (mmm) REVERT: 1 1438 MET cc_start: 0.8997 (mmp) cc_final: 0.8757 (mmm) REVERT: A 108 LEU cc_start: 0.9003 (tp) cc_final: 0.8787 (mt) REVERT: A 141 MET cc_start: 0.8933 (mtm) cc_final: 0.8726 (mtm) REVERT: B 128 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8690 (t80) outliers start: 9 outliers final: 0 residues processed: 110 average time/residue: 0.3778 time to fit residues: 59.1158 Evaluate side-chains 64 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 684 HIS 1 739 GLN ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS C 372 ASN C 450 ASN C 495 HIS A Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17401 Z= 0.286 Angle : 0.609 8.656 23626 Z= 0.319 Chirality : 0.042 0.153 2626 Planarity : 0.004 0.038 2972 Dihedral : 8.197 73.166 2483 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2006 helix: 1.61 (0.16), residues: 935 sheet: 0.16 (0.32), residues: 232 loop : 0.54 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 31 HIS 0.013 0.002 HIS 1 407 PHE 0.022 0.002 PHE B 75 TYR 0.029 0.002 TYR B 128 ARG 0.014 0.001 ARG 1 677 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 719 MET cc_start: 0.9100 (mtp) cc_final: 0.8613 (mmm) REVERT: 1 1438 MET cc_start: 0.8881 (mmp) cc_final: 0.8638 (mmm) REVERT: A 42 MET cc_start: 0.9240 (mmm) cc_final: 0.8998 (mmm) REVERT: A 184 ARG cc_start: 0.8299 (mtt-85) cc_final: 0.7862 (mtp85) REVERT: A 228 MET cc_start: 0.8702 (mmm) cc_final: 0.8479 (mmm) REVERT: C 378 SER cc_start: 0.9022 (p) cc_final: 0.8668 (p) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3273 time to fit residues: 36.7722 Evaluate side-chains 62 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 8.9990 chunk 57 optimal weight: 30.0000 chunk 154 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 353 GLN ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 679 ASN ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17401 Z= 0.245 Angle : 0.540 6.834 23626 Z= 0.281 Chirality : 0.040 0.155 2626 Planarity : 0.004 0.049 2972 Dihedral : 8.066 73.272 2483 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 2006 helix: 2.07 (0.17), residues: 936 sheet: 0.53 (0.32), residues: 239 loop : 0.72 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 1 671 HIS 0.014 0.001 HIS 1 407 PHE 0.017 0.002 PHE B 75 TYR 0.020 0.002 TYR B 128 ARG 0.005 0.001 ARG B 135 *********************** 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 68 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.088 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8517 (tpp) cc_final: 0.7724 (tpp) REVERT: 1 719 MET cc_start: 0.9003 (mtp) cc_final: 0.8443 (mmm) REVERT: 1 924 MET cc_start: 0.8757 (ttm) cc_final: 0.8553 (tpp) REVERT: 1 1376 MET cc_start: 0.7424 (mmp) cc_final: 0.6688 (mmm) REVERT: A 141 MET cc_start: 0.8964 (mtm) cc_final: 0.8632 (mtm) REVERT: A 184 ARG cc_start: 0.8379 (mtt-85) cc_final: 0.8041 (mtt-85) REVERT: A 319 LYS cc_start: 0.6452 (mttm) cc_final: 0.6090 (mttm) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3412 time to fit residues: 36.0794 Evaluate side-chains 57 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17401 Z= 0.234 Angle : 0.526 7.877 23626 Z= 0.270 Chirality : 0.040 0.164 2626 Planarity : 0.004 0.053 2972 Dihedral : 7.997 73.343 2483 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 2006 helix: 2.15 (0.17), residues: 937 sheet: 0.41 (0.32), residues: 231 loop : 0.78 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 671 HIS 0.004 0.001 HIS C 639 PHE 0.017 0.001 PHE B 75 TYR 0.032 0.001 TYR 11386 ARG 0.012 0.001 ARG 11276 *********************** 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 65 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.859 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8956 (ttm) cc_final: 0.8549 (tpp) REVERT: 1 719 MET cc_start: 0.9000 (mtp) cc_final: 0.8450 (mmm) REVERT: 1 919 GLU cc_start: 0.9645 (mt-10) cc_final: 0.9415 (mt-10) REVERT: 1 924 MET cc_start: 0.8785 (ttm) cc_final: 0.8337 (tpp) REVERT: A 114 MET cc_start: 0.8995 (tpp) cc_final: 0.8790 (tpp) REVERT: A 141 MET cc_start: 0.8986 (mtm) cc_final: 0.8720 (mtm) REVERT: A 184 ARG cc_start: 0.8407 (mtt-85) cc_final: 0.8041 (mtp85) REVERT: A 319 LYS cc_start: 0.6484 (mttm) cc_final: 0.6011 (mttm) REVERT: B 480 MET cc_start: 0.6859 (ttp) cc_final: 0.6591 (ttp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3044 time to fit residues: 31.4818 Evaluate side-chains 57 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 168 optimal weight: 0.0060 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 overall best weight: 5.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11036 ASN B 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17401 Z= 0.238 Angle : 0.523 7.204 23626 Z= 0.267 Chirality : 0.039 0.135 2626 Planarity : 0.004 0.054 2972 Dihedral : 8.008 73.301 2483 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.19), residues: 2006 helix: 2.15 (0.17), residues: 947 sheet: 0.24 (0.31), residues: 229 loop : 0.76 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 1 671 HIS 0.005 0.001 HIS C 692 PHE 0.019 0.001 PHE B 61 TYR 0.017 0.001 TYR B 128 ARG 0.019 0.001 ARG A 267 *********************** 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 63 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.983 Fit side-chains revert: symmetry clash REVERT: 1 719 MET cc_start: 0.9007 (mtp) cc_final: 0.8419 (mmm) REVERT: 1 919 GLU cc_start: 0.9640 (mt-10) cc_final: 0.9395 (mt-10) REVERT: A 42 MET cc_start: 0.9364 (mmm) cc_final: 0.9160 (mmm) REVERT: A 141 MET cc_start: 0.8986 (mtm) cc_final: 0.8639 (mtm) REVERT: A 184 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.7958 (mtt-85) REVERT: A 319 LYS cc_start: 0.6476 (mttm) cc_final: 0.6271 (mttm) REVERT: B 480 MET cc_start: 0.6903 (ttp) cc_final: 0.6561 (ttp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3037 time to fit residues: 30.8580 Evaluate side-chains 56 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 30.0000 chunk 177 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17401 Z= 0.209 Angle : 0.503 7.558 23626 Z= 0.258 Chirality : 0.039 0.144 2626 Planarity : 0.004 0.060 2972 Dihedral : 7.980 73.362 2483 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 2006 helix: 2.22 (0.17), residues: 948 sheet: 0.23 (0.32), residues: 229 loop : 0.76 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 671 HIS 0.008 0.001 HIS A 34 PHE 0.043 0.001 PHE B 132 TYR 0.015 0.001 TYR B 503 ARG 0.006 0.000 ARG A 177 *********************** 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 65 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8602 (tpp) cc_final: 0.8245 (tpp) REVERT: 1 719 MET cc_start: 0.9019 (mtp) cc_final: 0.8409 (mmm) REVERT: 1 919 GLU cc_start: 0.9633 (mt-10) cc_final: 0.9384 (mt-10) REVERT: A 141 MET cc_start: 0.8971 (mtm) cc_final: 0.8707 (mtm) REVERT: A 184 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8075 (mtp85) REVERT: A 319 LYS cc_start: 0.6539 (mttm) cc_final: 0.6235 (mttm) REVERT: B 480 MET cc_start: 0.6791 (ttp) cc_final: 0.6529 (ttp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3139 time to fit residues: 32.2455 Evaluate side-chains 56 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 50.0000 chunk 110 optimal weight: 0.9990 chunk 196 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 808 ASN B 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17401 Z= 0.160 Angle : 0.481 6.807 23626 Z= 0.247 Chirality : 0.039 0.142 2626 Planarity : 0.003 0.054 2972 Dihedral : 7.893 73.370 2483 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.19), residues: 2006 helix: 2.32 (0.17), residues: 952 sheet: 0.32 (0.31), residues: 237 loop : 0.80 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.006 0.001 HIS A 34 PHE 0.029 0.001 PHE B 132 TYR 0.014 0.001 TYR B 503 ARG 0.005 0.000 ARG B 135 *********************** 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 fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8565 (tpp) cc_final: 0.8279 (tpp) REVERT: 1 719 MET cc_start: 0.9023 (mtp) cc_final: 0.8429 (mmm) REVERT: 1 919 GLU cc_start: 0.9620 (mt-10) cc_final: 0.9383 (mt-10) REVERT: 1 924 MET cc_start: 0.8329 (tpp) cc_final: 0.7869 (tpp) REVERT: 1 1001 MET cc_start: 0.9438 (tpp) cc_final: 0.9209 (tpp) REVERT: A 42 MET cc_start: 0.9290 (mmm) cc_final: 0.9019 (mmm) REVERT: A 141 MET cc_start: 0.8929 (mtm) cc_final: 0.8666 (mtm) REVERT: A 184 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.7989 (mtt-85) REVERT: A 307 MET cc_start: 0.9203 (tpp) cc_final: 0.8916 (tpp) REVERT: B 480 MET cc_start: 0.6782 (ttp) cc_final: 0.6529 (ttp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3067 time to fit residues: 31.3200 Evaluate side-chains 53 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 712 GLN ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17401 Z= 0.233 Angle : 0.520 9.105 23626 Z= 0.266 Chirality : 0.039 0.137 2626 Planarity : 0.004 0.054 2972 Dihedral : 7.957 73.343 2483 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.19), residues: 2006 helix: 2.27 (0.17), residues: 954 sheet: 0.27 (0.32), residues: 234 loop : 0.77 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 1 671 HIS 0.004 0.001 HIS C 639 PHE 0.029 0.001 PHE B 132 TYR 0.016 0.001 TYR B 503 ARG 0.006 0.000 ARG A 207 *********************** 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 58 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 719 MET cc_start: 0.9020 (mtp) cc_final: 0.8310 (mmm) REVERT: 1 924 MET cc_start: 0.8318 (tpp) cc_final: 0.7908 (tpp) REVERT: 1 1001 MET cc_start: 0.9388 (tpp) cc_final: 0.9113 (tpp) REVERT: 1 1376 MET cc_start: 0.7917 (mmp) cc_final: 0.7712 (mmp) REVERT: A 42 MET cc_start: 0.9302 (mmm) cc_final: 0.9057 (mmm) REVERT: A 319 LYS cc_start: 0.6471 (mttm) cc_final: 0.5842 (mttp) REVERT: B 480 MET cc_start: 0.6821 (ttp) cc_final: 0.6569 (ttp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.3000 time to fit residues: 27.8394 Evaluate side-chains 53 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0570 chunk 171 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 173 optimal weight: 30.0000 chunk 182 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17401 Z= 0.159 Angle : 0.481 8.846 23626 Z= 0.246 Chirality : 0.039 0.137 2626 Planarity : 0.003 0.054 2972 Dihedral : 7.868 73.395 2483 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 2006 helix: 2.35 (0.17), residues: 950 sheet: 0.38 (0.32), residues: 238 loop : 0.85 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.004 0.001 HIS C 639 PHE 0.025 0.001 PHE B 116 TYR 0.014 0.001 TYR B 503 ARG 0.004 0.000 ARG B 135 *********************** 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 63 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 719 MET cc_start: 0.9015 (mtp) cc_final: 0.8287 (mmm) REVERT: 1 919 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9355 (mt-10) REVERT: 1 924 MET cc_start: 0.8266 (tpp) cc_final: 0.7919 (tpp) REVERT: 1 1001 MET cc_start: 0.9401 (tpp) cc_final: 0.9121 (tpp) REVERT: A 42 MET cc_start: 0.9338 (mmm) cc_final: 0.9052 (mmm) REVERT: A 184 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.7982 (mtt-85) REVERT: A 319 LYS cc_start: 0.6392 (mttm) cc_final: 0.5719 (mttp) REVERT: B 116 PHE cc_start: 0.6946 (p90) cc_final: 0.6452 (p90) REVERT: B 480 MET cc_start: 0.6747 (ttp) cc_final: 0.6202 (mtp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3024 time to fit residues: 30.5857 Evaluate side-chains 55 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 134 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17401 Z= 0.207 Angle : 0.504 8.866 23626 Z= 0.257 Chirality : 0.039 0.136 2626 Planarity : 0.003 0.056 2972 Dihedral : 7.893 73.361 2483 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.19), residues: 2006 helix: 2.33 (0.17), residues: 954 sheet: 0.36 (0.32), residues: 238 loop : 0.87 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 671 HIS 0.004 0.001 HIS C 639 PHE 0.029 0.001 PHE B 116 TYR 0.015 0.001 TYR B 503 ARG 0.004 0.000 ARG 11276 ********************** 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 57 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 619 MET cc_start: 0.8585 (tpp) cc_final: 0.8152 (mmt) REVERT: 1 719 MET cc_start: 0.8988 (mtp) cc_final: 0.8235 (mmm) REVERT: 1 863 MET cc_start: 0.7751 (mmm) cc_final: 0.7237 (mmm) REVERT: 1 924 MET cc_start: 0.8280 (tpp) cc_final: 0.7893 (tpp) REVERT: 1 1001 MET cc_start: 0.9390 (tpp) cc_final: 0.9131 (tpp) REVERT: 1 1376 MET cc_start: 0.7835 (mmp) cc_final: 0.7599 (mmp) REVERT: A 42 MET cc_start: 0.9350 (mmm) cc_final: 0.9064 (mmm) REVERT: A 319 LYS cc_start: 0.6464 (mttm) cc_final: 0.5752 (mttp) REVERT: B 480 MET cc_start: 0.6792 (ttp) cc_final: 0.6255 (mtp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3100 time to fit residues: 28.9698 Evaluate side-chains 54 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 29 optimal weight: 30.0000 chunk 142 optimal weight: 8.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.036642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.030196 restraints weight = 520432.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2334 r_free = 0.2334 target = 0.030706 restraints weight = 342801.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2334 r_free = 0.2334 target = 0.030747 restraints weight = 258793.757| |-----------------------------------------------------------------------------| 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-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: 6 | |-----------------------------------------------------------------------------| r_final: 0.2328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17401 Z= 0.213 Angle : 0.510 7.836 23626 Z= 0.259 Chirality : 0.039 0.135 2626 Planarity : 0.003 0.056 2972 Dihedral : 7.909 73.400 2483 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.19), residues: 2006 helix: 2.28 (0.17), residues: 954 sheet: 0.34 (0.32), residues: 236 loop : 0.84 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 671 HIS 0.005 0.001 HIS B 131 PHE 0.022 0.001 PHE B 132 TYR 0.016 0.001 TYR B 503 ARG 0.004 0.000 ARG 11276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2690.54 seconds wall clock time: 49 minutes 56.69 seconds (2996.69 seconds total)