Starting phenix.real_space_refine on Thu Aug 6 19:49:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8foh_29349/08_2026/8foh_29349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foh_29349/08_2026/8foh_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2026/8foh_29349.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2026/8foh_29349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2026/8foh_29349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2026/8foh_29349.map" model { file = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2026/8foh_29349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foh_29349/08_2026/8foh_29349.cif" } 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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: 6.12, per 1000 atoms: 0.36 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: 1.64 Conformation dependent library (CDL) restraints added in 1.1 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: 0.52 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: 3.39 Time building geometry restraints manager: 2.22 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' DC T 15 " pdb=" N1 DC T 15 " ideal model delta sigma weight residual 1.468 1.595 -0.127 1.40e-02 5.10e+03 8.17e+01 bond pdb=" C1' DC T 18 " pdb=" N1 DC T 18 " ideal model delta sigma weight residual 1.468 1.592 -0.124 1.40e-02 5.10e+03 7.86e+01 bond pdb=" C1' DC T 17 " pdb=" N1 DC T 17 " ideal model delta sigma weight residual 1.468 1.579 -0.111 1.40e-02 5.10e+03 6.23e+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=" C1' C P 4 " pdb=" N1 C P 4 " ideal model delta sigma weight residual 1.478 1.579 -0.101 2.00e-02 2.50e+03 2.53e+01 ... (remaining 17396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 21899 2.63 - 5.26: 1608 5.26 - 7.90: 87 7.90 - 10.53: 6 10.53 - 13.16: 26 Bond angle restraints: 23626 Sorted by residual: angle pdb=" C3' DT T 12 " pdb=" O3' DT T 12 " pdb=" P DG T 13 " ideal model delta sigma weight residual 119.70 107.37 12.33 1.20e+00 6.94e-01 1.06e+02 angle pdb=" C3' DG T 13 " pdb=" O3' DG T 13 " pdb=" P DC T 14 " ideal model delta sigma weight residual 119.70 108.11 11.59 1.20e+00 6.94e-01 9.33e+01 angle pdb=" C3' DG T 19 " pdb=" O3' DG T 19 " pdb=" P DC T 20 " ideal model delta sigma weight residual 119.70 108.61 11.09 1.20e+00 6.94e-01 8.53e+01 angle pdb=" C3' DG T 10 " pdb=" O3' DG T 10 " pdb=" P DC T 11 " ideal model delta sigma weight residual 119.70 109.04 10.66 1.20e+00 6.94e-01 7.90e+01 angle pdb=" C3' DC T 11 " pdb=" O3' DC T 11 " pdb=" P DT T 12 " ideal model delta sigma weight residual 119.70 109.08 10.62 1.20e+00 6.94e-01 7.84e+01 ... (remaining 23621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 9737 17.58 - 35.17: 622 35.17 - 52.75: 132 52.75 - 70.33: 29 70.33 - 87.91: 15 Dihedral angle restraints: 10535 sinusoidal: 4467 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 10532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2367 0.140 - 0.280: 231 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 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 22.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 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= 0.744 Angle : 1.469 13.159 23638 Z= 0.952 Chirality : 0.089 0.699 2626 Planarity : 0.011 0.218 2972 Dihedral : 12.903 87.912 6587 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 are 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/Z covalent geometry : bond 0.01296 / 0.74 (17401) covalent geometry : angle 1.46505 / 0.95 (23626) hydrogen bonds : bond 0.16423 / 11.33 ( 835) hydrogen bonds : angle 7.21691 / 5.07 ( 2356) metal coordination : bond 0.02834 / 1.22 ( 4) metal coordination : angle 5.04449 / 2.90 ( 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 : 0.691 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: 0.8783 (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: 0.1692 time to fit residues: 26.4890 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 : 0.526 ------------------------------------------------------------------------------- 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... ** 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 = 0.2700 r_free = 0.2700 target = 0.039484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.032383 restraints weight = 622504.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.032995 restraints weight = 371779.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.033169 restraints weight = 241157.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.033372 restraints weight = 203330.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.033457 restraints weight = 187668.761| |-----------------------------------------------------------------------------| r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 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 = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17405 Z= 0.196 Angle : 0.645 9.307 23638 Z= 0.336 Chirality : 0.043 0.142 2626 Planarity : 0.004 0.042 2972 Dihedral : 6.308 59.917 2445 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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 are not related in a simple way. whole: 1.38 (0.18), residues: 2006 helix: 1.61 (0.16), residues: 941 sheet: 0.24 (0.33), residues: 218 loop : 0.46 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 286 TYR 0.042 0.002 TYR B 128 PHE 0.018 0.002 PHE B 182 TRP 0.016 0.002 TRP B 439 HIS 0.015 0.002 HIS 1 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (17401) covalent geometry : angle 0.63722 / 0.34 (23626) hydrogen bonds : bond 0.04701 / 3.06 ( 835) hydrogen bonds : angle 5.33652 / 3.72 ( 2356) metal coordination : bond 0.00415 / 0.20 ( 4) metal coordination : angle 4.37314 / 2.32 ( 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 75 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 430 MET cc_start: 0.6292 (mmm) cc_final: 0.6051 (mmm) REVERT: 1 719 MET cc_start: 0.8841 (mtp) cc_final: 0.8464 (mmm) REVERT: 1 863 MET cc_start: 0.8204 (mmp) cc_final: 0.7955 (mmp) REVERT: 1 1001 MET cc_start: 0.9489 (mtm) cc_final: 0.9230 (mtp) REVERT: 1 1376 MET cc_start: 0.9241 (mmt) cc_final: 0.8519 (mmt) REVERT: A 42 MET cc_start: 0.9240 (mmm) cc_final: 0.9040 (mmm) REVERT: A 228 MET cc_start: 0.8729 (mmm) cc_final: 0.8477 (mmm) REVERT: B 162 MET cc_start: 0.9419 (mtp) cc_final: 0.9115 (mtm) REVERT: C 518 MET cc_start: 0.9596 (mmp) cc_final: 0.9340 (mmp) REVERT: C 690 TYR cc_start: 0.8871 (m-80) cc_final: 0.8602 (m-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1289 time to fit residues: 15.1091 Evaluate side-chains 62 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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: 9.9990 chunk 161 optimal weight: 4.9990 chunk 141 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 18 optimal weight: 0.0050 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 353 GLN ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2671 r_free = 0.2671 target = 0.038609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.031732 restraints weight = 491337.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.032250 restraints weight = 307921.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.032357 restraints weight = 230803.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.032464 restraints weight = 197322.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.032579 restraints weight = 186419.385| |-----------------------------------------------------------------------------| r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17405 Z= 0.151 Angle : 0.540 8.564 23638 Z= 0.280 Chirality : 0.041 0.144 2626 Planarity : 0.004 0.052 2972 Dihedral : 6.003 58.118 2445 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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 are not related in a simple way. whole: 1.89 (0.19), residues: 2006 helix: 2.03 (0.17), residues: 943 sheet: 0.39 (0.32), residues: 228 loop : 0.74 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 677 TYR 0.024 0.001 TYR B 128 PHE 0.021 0.002 PHE 1 355 TRP 0.014 0.001 TRP 1 671 HIS 0.014 0.001 HIS 1 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (17401) covalent geometry : angle 0.52932 / 0.28 (23626) hydrogen bonds : bond 0.03858 / 2.53 ( 835) hydrogen bonds : angle 4.92691 / 3.43 ( 2356) metal coordination : bond 0.00593 / 0.29 ( 4) metal coordination : angle 4.69495 / 2.57 ( 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 68 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8715 (tpp) cc_final: 0.8132 (tpp) REVERT: 1 430 MET cc_start: 0.6463 (mmm) cc_final: 0.6177 (mmm) REVERT: 1 626 MET cc_start: 0.9348 (mtt) cc_final: 0.9111 (mtt) REVERT: 1 719 MET cc_start: 0.8759 (mtp) cc_final: 0.8309 (mmm) REVERT: 1 863 MET cc_start: 0.8106 (mmp) cc_final: 0.7896 (mmp) REVERT: 1 1001 MET cc_start: 0.9444 (mtm) cc_final: 0.9203 (mtp) REVERT: 1 1376 MET cc_start: 0.9308 (mmt) cc_final: 0.8478 (mmm) REVERT: A 141 MET cc_start: 0.8639 (mtm) cc_final: 0.8360 (mtm) REVERT: A 228 MET cc_start: 0.8563 (mmm) cc_final: 0.8321 (mmm) REVERT: C 518 MET cc_start: 0.9516 (mmp) cc_final: 0.9239 (mmp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1393 time to fit residues: 14.5328 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 : 0.594 ------------------------------------------------------------------------------- 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: 20.0000 chunk 133 optimal weight: 0.9980 chunk 195 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 chunk 146 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 407 HIS 1 679 ASN ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.038415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.031379 restraints weight = 609803.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.032061 restraints weight = 346216.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.032118 restraints weight = 242772.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.032245 restraints weight = 204588.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.032374 restraints weight = 191720.041| |-----------------------------------------------------------------------------| r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2380 r_free = 0.2380 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2380 r_free = 0.2380 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17405 Z= 0.131 Angle : 0.511 8.397 23638 Z= 0.260 Chirality : 0.040 0.142 2626 Planarity : 0.003 0.056 2972 Dihedral : 5.916 59.525 2445 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 are not related in a simple way. whole: 2.11 (0.19), residues: 2006 helix: 2.26 (0.17), residues: 934 sheet: 0.52 (0.32), residues: 228 loop : 0.81 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 11276 TYR 0.023 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/Z covalent geometry : bond 0.00277 / 0.13 (17401) covalent geometry : angle 0.49885 / 0.26 (23626) hydrogen bonds : bond 0.03365 / 2.17 ( 835) hydrogen bonds : angle 4.74498 / 3.30 ( 2356) metal coordination : bond 0.00528 / 0.26 ( 4) metal coordination : angle 4.95564 / 2.74 ( 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 : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 719 MET cc_start: 0.8703 (mtp) cc_final: 0.8240 (mmm) REVERT: 1 863 MET cc_start: 0.8078 (mmp) cc_final: 0.7854 (mmp) REVERT: 1 924 MET cc_start: 0.8036 (ttm) cc_final: 0.7678 (tpp) REVERT: 1 1376 MET cc_start: 0.9312 (mmt) cc_final: 0.8370 (mmm) REVERT: A 114 MET cc_start: 0.8926 (tpt) cc_final: 0.8629 (mmm) REVERT: A 141 MET cc_start: 0.8657 (mtm) cc_final: 0.8340 (mtm) REVERT: A 184 ARG cc_start: 0.8973 (mtt-85) cc_final: 0.8189 (mtt-85) REVERT: A 228 MET cc_start: 0.8601 (mmm) cc_final: 0.8384 (mmm) REVERT: A 307 MET cc_start: 0.9100 (tpp) cc_final: 0.8860 (tpp) REVERT: A 319 LYS cc_start: 0.6150 (mttm) cc_final: 0.5869 (mttp) REVERT: B 117 ASN cc_start: 0.9100 (t0) cc_final: 0.8635 (p0) REVERT: C 518 MET cc_start: 0.9465 (mmp) cc_final: 0.9171 (mmp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1401 time to fit residues: 14.7741 Evaluate side-chains 59 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 0.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 187 optimal weight: 0.0170 chunk 122 optimal weight: 6.9990 chunk 63 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 overall best weight: 2.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2673 r_free = 0.2673 target = 0.038379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.031582 restraints weight = 572008.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.032079 restraints weight = 356592.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.032209 restraints weight = 255408.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.032552 restraints weight = 205642.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.032595 restraints weight = 184346.697| |-----------------------------------------------------------------------------| r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2388 r_free = 0.2388 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 = 0.2388 r_free = 0.2388 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17405 Z= 0.114 Angle : 0.487 8.631 23638 Z= 0.245 Chirality : 0.040 0.201 2626 Planarity : 0.003 0.056 2972 Dihedral : 5.838 59.796 2445 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.19), residues: 2006 helix: 2.36 (0.17), residues: 934 sheet: 0.60 (0.31), residues: 248 loop : 0.88 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 11276 TYR 0.017 0.001 TYR B 128 PHE 0.017 0.001 PHE B 75 TRP 0.009 0.001 TRP 1 671 HIS 0.006 0.001 HIS 1 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (17401) covalent geometry : angle 0.47384 / 0.25 (23626) hydrogen bonds : bond 0.03179 / 2.06 ( 835) hydrogen bonds : angle 4.62466 / 3.22 ( 2356) metal coordination : bond 0.00510 / 0.25 ( 4) metal coordination : angle 5.10326 / 2.83 ( 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 65 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 719 MET cc_start: 0.8831 (mtp) cc_final: 0.8362 (mmm) REVERT: 1 863 MET cc_start: 0.8097 (mmp) cc_final: 0.7869 (mmp) REVERT: 1 924 MET cc_start: 0.8086 (ttm) cc_final: 0.7801 (tpp) REVERT: 1 1376 MET cc_start: 0.9312 (mmt) cc_final: 0.8374 (mmm) REVERT: A 114 MET cc_start: 0.9042 (tpt) cc_final: 0.8767 (mmm) REVERT: A 141 MET cc_start: 0.8603 (mtm) cc_final: 0.8276 (mtm) REVERT: A 184 ARG cc_start: 0.8959 (mtt-85) cc_final: 0.8176 (mtp85) REVERT: A 228 MET cc_start: 0.8675 (mmm) cc_final: 0.8456 (mmm) REVERT: C 518 MET cc_start: 0.9429 (mmp) cc_final: 0.9123 (mmp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1293 time to fit residues: 13.3013 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 : 0.602 ------------------------------------------------------------------------------- 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: 8.9990 chunk 126 optimal weight: 9.9990 chunk 54 optimal weight: 40.0000 chunk 89 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.037257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.030620 restraints weight = 612555.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.030981 restraints weight = 390744.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.031197 restraints weight = 270471.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.031478 restraints weight = 213941.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.031578 restraints weight = 193457.939| |-----------------------------------------------------------------------------| r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2350 r_free = 0.2350 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 = 0.2350 r_free = 0.2350 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17405 Z= 0.212 Angle : 0.574 9.276 23638 Z= 0.289 Chirality : 0.041 0.254 2626 Planarity : 0.004 0.057 2972 Dihedral : 5.955 59.915 2445 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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 are not related in a simple way. whole: 2.01 (0.19), residues: 2006 helix: 2.20 (0.17), residues: 946 sheet: 0.23 (0.30), residues: 253 loop : 0.80 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 699 TYR 0.019 0.001 TYR B 128 PHE 0.019 0.002 PHE 11019 TRP 0.018 0.002 TRP 1 671 HIS 0.005 0.001 HIS C 639 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (17401) covalent geometry : angle 0.56140 / 0.29 (23626) hydrogen bonds : bond 0.03419 / 2.21 ( 835) hydrogen bonds : angle 4.75423 / 3.31 ( 2356) metal coordination : bond 0.00744 / 0.36 ( 4) metal coordination : angle 5.43648 / 3.04 ( 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 66 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 719 MET cc_start: 0.8754 (mtp) cc_final: 0.8290 (mmm) REVERT: 1 1001 MET cc_start: 0.9096 (ttt) cc_final: 0.8606 (tpp) REVERT: A 42 MET cc_start: 0.9227 (mmm) cc_final: 0.8868 (mmm) REVERT: A 114 MET cc_start: 0.9236 (tpt) cc_final: 0.8630 (tpp) REVERT: A 184 ARG cc_start: 0.8966 (mtt-85) cc_final: 0.8227 (mtp85) REVERT: A 228 MET cc_start: 0.8753 (mmm) cc_final: 0.8529 (mmm) REVERT: A 319 LYS cc_start: 0.6307 (mttm) cc_final: 0.5988 (mttm) REVERT: B 56 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8700 (mp0) REVERT: C 518 MET cc_start: 0.9377 (mmp) cc_final: 0.9108 (mmp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1267 time to fit residues: 13.1843 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 : 0.463 ------------------------------------------------------------------------------- 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: 6.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 43 optimal weight: 30.0000 chunk 203 optimal weight: 40.0000 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 0.0270 chunk 48 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 638 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 = 0.2658 r_free = 0.2658 target = 0.037775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.031290 restraints weight = 514202.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.031827 restraints weight = 341731.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.031925 restraints weight = 251223.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.032050 restraints weight = 197047.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.032263 restraints weight = 182607.094| |-----------------------------------------------------------------------------| 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 = 0.01 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-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: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17405 Z= 0.115 Angle : 0.501 9.307 23638 Z= 0.252 Chirality : 0.040 0.136 2626 Planarity : 0.003 0.057 2972 Dihedral : 5.868 59.876 2445 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.19), residues: 2006 helix: 2.35 (0.17), residues: 937 sheet: 0.41 (0.31), residues: 241 loop : 0.89 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 177 TYR 0.026 0.001 TYR B 128 PHE 0.035 0.001 PHE B 132 TRP 0.008 0.001 TRP 1 671 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17401) covalent geometry : angle 0.48314 / 0.25 (23626) hydrogen bonds : bond 0.03105 / 2.03 ( 835) hydrogen bonds : angle 4.62813 / 3.24 ( 2356) metal coordination : bond 0.00730 / 0.36 ( 4) metal coordination : angle 5.85953 / 3.30 ( 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 64 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8264 (tpt) cc_final: 0.8008 (tpt) REVERT: 1 719 MET cc_start: 0.8767 (mtp) cc_final: 0.8295 (mmm) REVERT: 1 919 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9398 (mt-10) REVERT: A 42 MET cc_start: 0.9212 (mmm) cc_final: 0.8870 (mmm) REVERT: A 114 MET cc_start: 0.9281 (tpt) cc_final: 0.8677 (tpp) REVERT: A 228 MET cc_start: 0.8936 (mmm) cc_final: 0.8723 (mmm) REVERT: A 319 LYS cc_start: 0.6254 (mttm) cc_final: 0.6009 (mttp) REVERT: C 518 MET cc_start: 0.9361 (mmp) cc_final: 0.9091 (mmp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1091 time to fit residues: 11.2130 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 : 0.627 ------------------------------------------------------------------------------- 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: 0.0970 chunk 86 optimal weight: 30.0000 chunk 78 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 808 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.037463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.030967 restraints weight = 527459.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.031490 restraints weight = 349778.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.031609 restraints weight = 254065.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.031688 restraints weight = 204927.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.031856 restraints weight = 189422.958| |-----------------------------------------------------------------------------| r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2368 r_free = 0.2368 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2368 r_free = 0.2368 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17405 Z= 0.149 Angle : 0.515 9.445 23638 Z= 0.258 Chirality : 0.040 0.147 2626 Planarity : 0.003 0.057 2972 Dihedral : 5.852 59.916 2445 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 2006 helix: 2.31 (0.17), residues: 945 sheet: 0.34 (0.32), residues: 231 loop : 0.81 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 11276 TYR 0.014 0.001 TYR B 503 PHE 0.031 0.001 PHE B 132 TRP 0.013 0.001 TRP 1 671 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (17401) covalent geometry : angle 0.49835 / 0.26 (23626) hydrogen bonds : bond 0.03095 / 2.02 ( 835) hydrogen bonds : angle 4.62658 / 3.24 ( 2356) metal coordination : bond 0.00640 / 0.32 ( 4) metal coordination : angle 5.86202 / 3.31 ( 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 63 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8237 (tpt) cc_final: 0.7952 (tpt) REVERT: 1 719 MET cc_start: 0.8716 (mtp) cc_final: 0.8233 (mmm) REVERT: 1 749 MET cc_start: 0.9472 (mtp) cc_final: 0.9270 (mtm) REVERT: 1 919 GLU cc_start: 0.9685 (mt-10) cc_final: 0.9410 (mt-10) REVERT: 1 1001 MET cc_start: 0.8971 (ttt) cc_final: 0.8534 (tpp) REVERT: A 42 MET cc_start: 0.9277 (mmm) cc_final: 0.8932 (mmm) REVERT: A 114 MET cc_start: 0.9338 (tpt) cc_final: 0.8751 (tpp) REVERT: A 141 MET cc_start: 0.8638 (mtm) cc_final: 0.8153 (mtm) REVERT: A 184 ARG cc_start: 0.8976 (mtt-85) cc_final: 0.8241 (mtp85) REVERT: A 228 MET cc_start: 0.9033 (mmm) cc_final: 0.8824 (mmm) REVERT: C 518 MET cc_start: 0.9360 (mmp) cc_final: 0.9111 (mmp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1078 time to fit residues: 10.9510 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 : 0.517 ------------------------------------------------------------------------------- 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: 9.9990 chunk 121 optimal weight: 0.0060 chunk 107 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 chunk 153 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 overall best weight: 5.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2640 r_free = 0.2640 target = 0.037211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.030731 restraints weight = 513545.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.031220 restraints weight = 329090.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.031276 restraints weight = 258833.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.031396 restraints weight = 202629.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.031623 restraints weight = 188252.904| |-----------------------------------------------------------------------------| r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2360 r_free = 0.2360 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 = 0.2360 r_free = 0.2360 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17405 Z= 0.152 Angle : 0.518 9.767 23638 Z= 0.260 Chirality : 0.040 0.137 2626 Planarity : 0.003 0.056 2972 Dihedral : 5.839 59.978 2445 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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 are not related in a simple way. whole: 2.13 (0.19), residues: 2006 helix: 2.30 (0.17), residues: 945 sheet: 0.33 (0.32), residues: 231 loop : 0.83 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 177 TYR 0.015 0.001 TYR B 503 PHE 0.032 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/Z covalent geometry : bond 0.00323 / 0.15 (17401) covalent geometry : angle 0.49936 / 0.26 (23626) hydrogen bonds : bond 0.03073 / 1.99 ( 835) hydrogen bonds : angle 4.63005 / 3.24 ( 2356) metal coordination : bond 0.00701 / 0.35 ( 4) metal coordination : angle 6.07341 / 3.43 ( 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 : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8304 (tpt) cc_final: 0.8037 (tpt) REVERT: 1 719 MET cc_start: 0.8719 (mtp) cc_final: 0.8241 (mmm) REVERT: 1 988 MET cc_start: 0.8978 (ttm) cc_final: 0.8712 (ttm) REVERT: 1 1376 MET cc_start: 0.8135 (mmp) cc_final: 0.7900 (mmp) REVERT: A 42 MET cc_start: 0.9319 (mmm) cc_final: 0.8961 (mmm) REVERT: A 114 MET cc_start: 0.9396 (tpt) cc_final: 0.8837 (tpp) REVERT: A 141 MET cc_start: 0.8674 (mtm) cc_final: 0.8204 (mtm) REVERT: A 184 ARG cc_start: 0.8958 (mtt-85) cc_final: 0.8235 (mtp85) REVERT: C 518 MET cc_start: 0.9374 (mmp) cc_final: 0.9127 (mmp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1096 time to fit residues: 10.7069 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 : 0.440 ------------------------------------------------------------------------------- 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: 4.9990 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 114 optimal weight: 0.0870 chunk 106 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 overall best weight: 3.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2644 r_free = 0.2644 target = 0.037281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.030690 restraints weight = 603923.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.031218 restraints weight = 374223.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.031432 restraints weight = 256012.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.031519 restraints weight = 207656.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.031697 restraints weight = 191671.434| |-----------------------------------------------------------------------------| r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2368 r_free = 0.2368 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2368 r_free = 0.2368 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17405 Z= 0.134 Angle : 0.516 9.918 23638 Z= 0.258 Chirality : 0.040 0.169 2626 Planarity : 0.003 0.056 2972 Dihedral : 5.823 59.944 2445 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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 are not related in a simple way. whole: 2.13 (0.19), residues: 2006 helix: 2.29 (0.17), residues: 945 sheet: 0.29 (0.32), residues: 231 loop : 0.87 (0.23), residues: 830 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 0.030 0.001 PHE B 132 TRP 0.012 0.001 TRP 1 671 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (17401) covalent geometry : angle 0.49636 / 0.26 (23626) hydrogen bonds : bond 0.03055 / 1.98 ( 835) hydrogen bonds : angle 4.64679 / 3.26 ( 2356) metal coordination : bond 0.00664 / 0.33 ( 4) metal coordination : angle 6.23719 / 3.53 ( 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 59 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8281 (tpt) cc_final: 0.8025 (tpt) REVERT: 1 719 MET cc_start: 0.8701 (mtp) cc_final: 0.8223 (mmm) REVERT: 1 919 GLU cc_start: 0.9666 (mt-10) cc_final: 0.9409 (mt-10) REVERT: 1 924 MET cc_start: 0.7236 (mmt) cc_final: 0.7009 (mmt) REVERT: 1 1059 ASN cc_start: 0.9529 (t0) cc_final: 0.9295 (t0) REVERT: A 42 MET cc_start: 0.9345 (mmm) cc_final: 0.9027 (mmm) REVERT: A 114 MET cc_start: 0.9412 (tpt) cc_final: 0.8873 (tpp) REVERT: A 141 MET cc_start: 0.8641 (mtm) cc_final: 0.8153 (mtm) REVERT: A 184 ARG cc_start: 0.8991 (mtt-85) cc_final: 0.8276 (mtp85) REVERT: C 518 MET cc_start: 0.9342 (mmp) cc_final: 0.8988 (mmm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1195 time to fit residues: 11.6868 Evaluate side-chains 51 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 30 optimal weight: 50.0000 chunk 165 optimal weight: 0.0270 chunk 72 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 overall best weight: 4.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.037130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2333 r_free = 0.2333 target = 0.030538 restraints weight = 607863.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.031110 restraints weight = 372424.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.031287 restraints weight = 256039.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.031351 restraints weight = 206679.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.031625 restraints weight = 191522.649| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17405 Z= 0.137 Angle : 0.521 10.224 23638 Z= 0.260 Chirality : 0.040 0.232 2626 Planarity : 0.003 0.056 2972 Dihedral : 5.808 59.744 2445 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.49 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 are not related in a simple way. whole: 2.13 (0.19), residues: 2006 helix: 2.31 (0.17), residues: 948 sheet: 0.24 (0.32), residues: 240 loop : 0.86 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 177 TYR 0.015 0.001 TYR B 503 PHE 0.031 0.001 PHE B 132 TRP 0.013 0.001 TRP 1 671 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (17401) covalent geometry : angle 0.50119 / 0.26 (23626) hydrogen bonds : bond 0.03028 / 1.97 ( 835) hydrogen bonds : angle 4.62994 / 3.25 ( 2356) metal coordination : bond 0.00659 / 0.32 ( 4) metal coordination : angle 6.34124 / 3.60 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.31 seconds wall clock time: 38 minutes 15.39 seconds (2295.39 seconds total)