Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 08:09:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/04_2023/7xsr_33432.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/04_2023/7xsr_33432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/04_2023/7xsr_33432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/04_2023/7xsr_33432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/04_2023/7xsr_33432.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/04_2023/7xsr_33432.pdb" } resolution = 2.97 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.044 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 Zn 4 6.06 5 P 49 5.49 5 S 57 5.16 5 C 10558 2.51 5 N 2934 2.21 5 O 3305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ASP 520": "OD1" <-> "OD2" Residue "B ASP 547": "OD1" <-> "OD2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 624": "OE1" <-> "OE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B ASP 698": "OD1" <-> "OD2" Residue "B ASP 709": "OD1" <-> "OD2" Residue "B ASP 741": "OD1" <-> "OD2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B GLU 763": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B ASP 788": "OD1" <-> "OD2" Residue "B ASP 801": "OD1" <-> "OD2" Residue "B ASP 806": "OD1" <-> "OD2" Residue "B ASP 833": "OD1" <-> "OD2" Residue "B ASP 847": "OD1" <-> "OD2" Residue "B ASP 869": "OD1" <-> "OD2" Residue "B ASP 875": "OD1" <-> "OD2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 938": "OD1" <-> "OD2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "B ASP 971": "OD1" <-> "OD2" Residue "B PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1024": "OE1" <-> "OE2" Residue "B ASP 1025": "OD1" <-> "OD2" Residue "B ASP 1411": "OD1" <-> "OD2" Residue "B ASP 1471": "OD1" <-> "OD2" Residue "B GLU 1496": "OE1" <-> "OE2" Residue "B GLU 1499": "OE1" <-> "OE2" Residue "B GLU 1504": "OE1" <-> "OE2" Residue "B ASP 1521": "OD1" <-> "OD2" Residue "B ASP 1565": "OD1" <-> "OD2" Residue "B PHE 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1577": "OD1" <-> "OD2" Residue "B GLU 1589": "OE1" <-> "OE2" Residue "B GLU 1600": "OE1" <-> "OE2" Residue "B ASP 1670": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C ASP 302": "OD1" <-> "OD2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C ASP 330": "OD1" <-> "OD2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C ASP 338": "OD1" <-> "OD2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C ASP 543": "OD1" <-> "OD2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 548": "OE1" <-> "OE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C GLU 609": "OE1" <-> "OE2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C GLU 674": "OE1" <-> "OE2" Residue "C GLU 678": "OE1" <-> "OE2" Residue "C GLU 681": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16907 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 10378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1287, 10378 Classifications: {'peptide': 1287} Link IDs: {'PTRANS': 60, 'TRANS': 1226} Chain breaks: 3 Chain: "C" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5482 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain breaks: 1 Chain: "A" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 676 SG CYS B 88 90.553 35.311 38.173 1.00 33.30 S ATOM 947 SG CYS B 121 94.678 33.022 37.660 1.00 41.85 S ATOM 993 SG CYS B 127 94.923 36.292 40.080 1.00 31.93 S ATOM 1017 SG CYS B 130 92.866 33.583 41.273 1.00 29.20 S ATOM 3755 SG CYS B 491 64.651 52.396 51.436 1.00 34.19 S ATOM 3837 SG CYS B 503 66.139 54.198 48.666 1.00 31.01 S ATOM 3859 SG CYS B 506 69.366 52.378 51.448 1.00 29.73 S ATOM 5830 SG CYS B 750 41.081 64.124 69.071 1.00 47.55 S ATOM 5843 SG CYS B 752 42.051 68.235 68.440 1.00 40.60 S ATOM 5865 SG CYS B 755 44.819 66.200 69.641 1.00 34.26 S ATOM 7868 SG CYS B1018 35.862 82.640 102.441 1.00 31.62 S ATOM 8039 SG CYS B1406 35.145 79.400 100.591 1.00 35.05 S ATOM 8090 SG CYS B1414 33.705 83.417 98.992 1.00 31.82 S ATOM 8107 SG CYS B1417 37.109 82.215 98.694 1.00 28.08 S Time building chain proxies: 9.00, per 1000 atoms: 0.53 Number of scatterers: 16907 At special positions: 0 Unit cell: (118.845, 136.8, 143.64, 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) Zn 4 29.99 S 57 16.00 P 49 15.00 O 3305 8.00 N 2934 7.00 C 10558 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 - 3.50 Amino acid : False - 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: 6.20 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 130 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 88 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 506 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 491 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 752 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 755 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1406 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1417 " Number of angles added : 15 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 20 sheets defined 39.3% alpha, 17.3% beta 5 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.786A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.871A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.331A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 354 through 375 removed outlier: 3.508A pdb=" N PHE B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 488 removed outlier: 3.614A pdb=" N LEU B 475 " --> pdb=" O PRO B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.792A pdb=" N LEU B 634 " --> pdb=" O LYS B 630 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.724A pdb=" N LEU B 658 " --> pdb=" O ARG B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.770A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 759 Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 855 through 859 Processing helix chain 'B' and resid 873 through 883 Processing helix chain 'B' and resid 999 through 1015 removed outlier: 3.802A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1404 removed outlier: 3.720A pdb=" N HIS B1404 " --> pdb=" O LYS B1401 " (cutoff:3.500A) Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.212A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.942A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1499 Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.505A pdb=" N ILE B1587 " --> pdb=" O PRO B1583 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.659A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1673 through 1683 removed outlier: 3.570A pdb=" N THR B1683 " --> pdb=" O LYS B1679 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 33 Processing helix chain 'C' and resid 37 through 59 Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.757A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 109 removed outlier: 3.811A pdb=" N LYS C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 136 Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 163 through 177 removed outlier: 4.107A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.258A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.982A pdb=" N ILE C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 302 through 322 removed outlier: 3.845A pdb=" N LYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 340 through 362 removed outlier: 3.975A pdb=" N TYR C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 451 removed outlier: 3.517A pdb=" N PHE C 437 " --> pdb=" O TYR C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 490 through 494 Processing helix chain 'C' and resid 509 through 513 removed outlier: 3.688A pdb=" N GLU C 512 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 513 " --> pdb=" O PHE C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 509 through 513' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 547 through 552 Processing helix chain 'C' and resid 566 through 571 Processing helix chain 'C' and resid 592 through 596 removed outlier: 3.710A pdb=" N SER C 596 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 613 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.851A pdb=" N ALA C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 679 removed outlier: 3.849A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 691 removed outlier: 4.032A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.718A pdb=" N PHE C 703 " --> pdb=" O HIS C 699 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.748A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 19 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP B 44 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 21 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N TRP B 46 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 13.887A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP B 190 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 192 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.922A pdb=" N LEU B 167 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR B 9 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.627A pdb=" N VAL B 85 " --> pdb=" O TRP B 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.355A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.753A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY B 600 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.753A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.693A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AB1, first strand: chain 'B' and resid 533 through 534 removed outlier: 3.726A pdb=" N THR B 539 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.542A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.542A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 699 through 700 removed outlier: 6.942A pdb=" N ALA B 699 " --> pdb=" O TYR B 808 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.975A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.975A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS B 957 " --> pdb=" O ILE B1564 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE B1564 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU B 959 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE B1562 " --> pdb=" O GLU B 959 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 985 through 986 removed outlier: 6.469A pdb=" N LYS B 985 " --> pdb=" O THR B1508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 425 through 431 removed outlier: 3.588A pdb=" N PHE C 405 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 562 through 563 removed outlier: 7.961A pdb=" N LYS C 562 " --> pdb=" O TYR C 536 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C 538 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR C 660 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 586 through 587 666 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 7.63 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3255 1.33 - 1.45: 4542 1.45 - 1.57: 9445 1.57 - 1.69: 62 1.69 - 1.81: 80 Bond restraints: 17384 Sorted by residual: bond pdb=" O3' G A 27 " pdb=" P C A 28 " ideal model delta sigma weight residual 1.607 1.475 0.132 1.50e-02 4.44e+03 7.70e+01 bond pdb=" O3' C D 9 " pdb=" P U D 10 " ideal model delta sigma weight residual 1.607 1.481 0.126 1.50e-02 4.44e+03 7.03e+01 bond pdb=" O3' U D 8 " pdb=" P C D 9 " ideal model delta sigma weight residual 1.607 1.488 0.119 1.50e-02 4.44e+03 6.31e+01 bond pdb=" O3' U D -2 " pdb=" P A D -1 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.50e-02 4.44e+03 6.03e+01 bond pdb=" O3' G D -9 " pdb=" P U D -8 " ideal model delta sigma weight residual 1.607 1.493 0.114 1.50e-02 4.44e+03 5.77e+01 ... (remaining 17379 not shown) Histogram of bond angle deviations from ideal: 91.70 - 100.38: 19 100.38 - 109.06: 1772 109.06 - 117.74: 11305 117.74 - 126.43: 10136 126.43 - 135.11: 441 Bond angle restraints: 23673 Sorted by residual: angle pdb=" O3' C D 13 " pdb=" C3' C D 13 " pdb=" C2' C D 13 " ideal model delta sigma weight residual 113.70 132.27 -18.57 1.50e+00 4.44e-01 1.53e+02 angle pdb=" O2' C D 1 " pdb=" C2' C D 1 " pdb=" C1' C D 1 " ideal model delta sigma weight residual 108.40 91.70 16.70 1.50e+00 4.44e-01 1.24e+02 angle pdb=" O2' U D -2 " pdb=" C2' U D -2 " pdb=" C1' U D -2 " ideal model delta sigma weight residual 111.80 100.28 11.52 1.50e+00 4.44e-01 5.89e+01 angle pdb=" O4' A D -1 " pdb=" C1' A D -1 " pdb=" C2' A D -1 " ideal model delta sigma weight residual 105.80 99.29 6.51 1.00e+00 1.00e+00 4.23e+01 angle pdb=" O2' C D -7 " pdb=" C2' C D -7 " pdb=" C1' C D -7 " ideal model delta sigma weight residual 108.40 117.85 -9.45 1.50e+00 4.44e-01 3.97e+01 ... (remaining 23668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 9914 33.72 - 67.43: 404 67.43 - 101.15: 26 101.15 - 134.87: 2 134.87 - 168.58: 4 Dihedral angle restraints: 10350 sinusoidal: 4691 harmonic: 5659 Sorted by residual: dihedral pdb=" O4' U D -13 " pdb=" C1' U D -13 " pdb=" N1 U D -13 " pdb=" C2 U D -13 " ideal model delta sinusoidal sigma weight residual -160.00 5.71 -165.71 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 50.53 149.47 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 40.58 -168.58 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2518 0.181 - 0.363: 40 0.363 - 0.544: 3 0.544 - 0.725: 1 0.725 - 0.907: 1 Chirality restraints: 2563 Sorted by residual: chirality pdb=" C3' C D 13 " pdb=" C4' C D 13 " pdb=" O3' C D 13 " pdb=" C2' C D 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.57 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" C2' C D -7 " pdb=" C3' C D -7 " pdb=" O2' C D -7 " pdb=" C1' C D -7 " both_signs ideal model delta sigma weight residual False -2.75 -2.19 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C2' C D 13 " pdb=" C3' C D 13 " pdb=" O2' C D 13 " pdb=" C1' C D 13 " both_signs ideal model delta sigma weight residual False -2.75 -2.32 -0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 2560 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D -1 " 0.093 2.00e-02 2.50e+03 4.23e-02 4.93e+01 pdb=" N9 A D -1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 A D -1 " 0.008 2.00e-02 2.50e+03 pdb=" N7 A D -1 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D -1 " -0.010 2.00e-02 2.50e+03 pdb=" C6 A D -1 " 0.029 2.00e-02 2.50e+03 pdb=" N6 A D -1 " 0.013 2.00e-02 2.50e+03 pdb=" N1 A D -1 " 0.020 2.00e-02 2.50e+03 pdb=" C2 A D -1 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A D -1 " -0.021 2.00e-02 2.50e+03 pdb=" C4 A D -1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 34 " 0.077 2.00e-02 2.50e+03 3.25e-02 2.90e+01 pdb=" N9 A A 34 " -0.048 2.00e-02 2.50e+03 pdb=" C8 A A 34 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A A 34 " -0.009 2.00e-02 2.50e+03 pdb=" C5 A A 34 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A A 34 " 0.017 2.00e-02 2.50e+03 pdb=" N6 A A 34 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A 34 " 0.027 2.00e-02 2.50e+03 pdb=" C2 A A 34 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A A 34 " -0.032 2.00e-02 2.50e+03 pdb=" C4 A A 34 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 442 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C LYS B 442 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS B 442 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU B 443 " -0.023 2.00e-02 2.50e+03 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4099 2.79 - 3.32: 13688 3.32 - 3.85: 26543 3.85 - 4.37: 30891 4.37 - 4.90: 54969 Nonbonded interactions: 130190 Sorted by model distance: nonbonded pdb=" OG SER B 378 " pdb=" OD1 ASN B 453 " model vdw 2.268 2.440 nonbonded pdb=" O ASN B 179 " pdb=" O2' G D -3 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR B1645 " pdb=" OP1 C D 14 " model vdw 2.328 2.440 nonbonded pdb=" O THR C 702 " pdb=" OG SER C 706 " model vdw 2.329 2.440 nonbonded pdb=" OH TYR B 191 " pdb=" OD1 ASP B 386 " model vdw 2.333 2.440 ... (remaining 130185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.170 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 50.870 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.007 0.132 17384 Z= 0.464 Angle : 0.969 18.809 23673 Z= 0.568 Chirality : 0.066 0.907 2563 Planarity : 0.008 0.088 2873 Dihedral : 17.322 168.585 6714 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 1951 helix: -1.57 (0.15), residues: 692 sheet: 0.06 (0.31), residues: 267 loop : -2.35 (0.15), residues: 992 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 414 time to evaluate : 2.103 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 15 residues processed: 466 average time/residue: 1.3388 time to fit residues: 691.5048 Evaluate side-chains 355 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 340 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 5 average time/residue: 0.2080 time to fit residues: 4.4119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN B 348 GLN B 434 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 ASN B 900 ASN B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1404 HIS B1596 GLN B1604 ASN C 147 ASN C 183 HIS C 513 ASN C 552 ASN C 572 ASN C 592 ASN C 602 ASN C 642 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 17384 Z= 0.185 Angle : 0.568 11.402 23673 Z= 0.298 Chirality : 0.041 0.218 2563 Planarity : 0.005 0.071 2873 Dihedral : 11.633 175.520 2709 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.41 % Rotamer Outliers : 4.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 1951 helix: 0.65 (0.19), residues: 703 sheet: 0.34 (0.31), residues: 258 loop : -1.88 (0.16), residues: 990 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 361 time to evaluate : 1.951 Fit side-chains outliers start: 85 outliers final: 35 residues processed: 409 average time/residue: 1.4165 time to fit residues: 642.1446 Evaluate side-chains 371 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 336 time to evaluate : 2.023 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 24 residues processed: 13 average time/residue: 0.4960 time to fit residues: 11.2150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 179 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 112 GLN B 348 GLN B 498 GLN B 673 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 871 ASN B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 924 HIS B1573 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 17384 Z= 0.284 Angle : 0.612 10.623 23673 Z= 0.319 Chirality : 0.044 0.204 2563 Planarity : 0.005 0.071 2873 Dihedral : 11.617 172.844 2709 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.26 % Rotamer Outliers : 6.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 1951 helix: 1.31 (0.20), residues: 696 sheet: 0.40 (0.31), residues: 264 loop : -1.73 (0.17), residues: 991 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 366 time to evaluate : 2.080 Fit side-chains revert: symmetry clash outliers start: 108 outliers final: 54 residues processed: 423 average time/residue: 1.3359 time to fit residues: 628.2638 Evaluate side-chains 399 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 345 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 33 residues processed: 22 average time/residue: 0.7975 time to fit residues: 23.3583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1584 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 642 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17384 Z= 0.174 Angle : 0.538 9.884 23673 Z= 0.280 Chirality : 0.041 0.167 2563 Planarity : 0.005 0.066 2873 Dihedral : 11.465 174.462 2709 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.82 % Rotamer Outliers : 5.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 1951 helix: 1.68 (0.20), residues: 702 sheet: 0.49 (0.31), residues: 263 loop : -1.60 (0.17), residues: 986 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 348 time to evaluate : 1.830 Fit side-chains revert: symmetry clash outliers start: 99 outliers final: 50 residues processed: 408 average time/residue: 1.3613 time to fit residues: 616.2130 Evaluate side-chains 385 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 335 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 31 residues processed: 20 average time/residue: 0.4423 time to fit residues: 14.4485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 0.9990 chunk 109 optimal weight: 0.0010 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 615 ASN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 17384 Z= 0.221 Angle : 0.566 13.544 23673 Z= 0.293 Chirality : 0.042 0.157 2563 Planarity : 0.005 0.065 2873 Dihedral : 11.459 173.600 2709 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer Outliers : 5.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 1951 helix: 1.71 (0.20), residues: 705 sheet: 0.58 (0.31), residues: 265 loop : -1.57 (0.17), residues: 981 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 348 time to evaluate : 1.913 Fit side-chains outliers start: 90 outliers final: 57 residues processed: 399 average time/residue: 1.4521 time to fit residues: 642.8005 Evaluate side-chains 400 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 343 time to evaluate : 1.939 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 40 residues processed: 21 average time/residue: 0.6459 time to fit residues: 19.1202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 1.9990 chunk 173 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 348 GLN B 615 ASN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 642 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 17384 Z= 0.269 Angle : 0.597 12.878 23673 Z= 0.309 Chirality : 0.043 0.191 2563 Planarity : 0.005 0.065 2873 Dihedral : 11.524 173.510 2709 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.05 % Rotamer Outliers : 5.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 1951 helix: 1.65 (0.19), residues: 704 sheet: 0.60 (0.31), residues: 265 loop : -1.60 (0.17), residues: 982 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 340 time to evaluate : 1.997 Fit side-chains outliers start: 89 outliers final: 55 residues processed: 394 average time/residue: 1.4003 time to fit residues: 612.2712 Evaluate side-chains 396 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 341 time to evaluate : 1.963 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 42 residues processed: 15 average time/residue: 0.5957 time to fit residues: 13.8194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 107 optimal weight: 0.2980 chunk 191 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 116 optimal weight: 0.0970 chunk 88 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 615 ASN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 17384 Z= 0.159 Angle : 0.543 12.780 23673 Z= 0.281 Chirality : 0.040 0.169 2563 Planarity : 0.004 0.064 2873 Dihedral : 11.402 174.788 2709 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer Outliers : 4.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 1951 helix: 1.87 (0.20), residues: 703 sheet: 0.62 (0.31), residues: 265 loop : -1.52 (0.17), residues: 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 341 time to evaluate : 1.928 Fit side-chains revert: symmetry clash outliers start: 85 outliers final: 53 residues processed: 389 average time/residue: 1.4175 time to fit residues: 613.6214 Evaluate side-chains 389 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 336 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 39 residues processed: 16 average time/residue: 0.7307 time to fit residues: 16.7738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 348 GLN B 498 GLN B 534 ASN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN C 357 GLN C 541 ASN C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 17384 Z= 0.229 Angle : 0.587 13.041 23673 Z= 0.302 Chirality : 0.042 0.159 2563 Planarity : 0.005 0.064 2873 Dihedral : 11.437 174.061 2709 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer Outliers : 4.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 1951 helix: 1.80 (0.20), residues: 704 sheet: 0.59 (0.31), residues: 265 loop : -1.54 (0.17), residues: 982 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 339 time to evaluate : 1.924 Fit side-chains revert: symmetry clash outliers start: 76 outliers final: 51 residues processed: 386 average time/residue: 1.3944 time to fit residues: 597.4287 Evaluate side-chains 387 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 336 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 40 residues processed: 13 average time/residue: 0.8004 time to fit residues: 15.0923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 434 GLN B 498 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN C 541 ASN C 575 ASN C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 17384 Z= 0.223 Angle : 0.590 12.873 23673 Z= 0.304 Chirality : 0.042 0.172 2563 Planarity : 0.005 0.064 2873 Dihedral : 11.435 174.294 2709 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 1951 helix: 1.75 (0.20), residues: 706 sheet: 0.58 (0.31), residues: 265 loop : -1.52 (0.17), residues: 980 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 335 time to evaluate : 1.940 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 51 residues processed: 381 average time/residue: 1.4114 time to fit residues: 597.5593 Evaluate side-chains 388 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 337 time to evaluate : 1.918 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 41 residues processed: 12 average time/residue: 0.6067 time to fit residues: 11.7556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 0.0870 chunk 168 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 348 GLN B 498 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN C 541 ASN C 642 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 17384 Z= 0.291 Angle : 0.637 13.027 23673 Z= 0.328 Chirality : 0.044 0.191 2563 Planarity : 0.005 0.065 2873 Dihedral : 11.506 173.555 2709 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 1951 helix: 1.66 (0.20), residues: 705 sheet: 0.59 (0.31), residues: 265 loop : -1.58 (0.17), residues: 981 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 334 time to evaluate : 2.090 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 48 residues processed: 378 average time/residue: 1.4611 time to fit residues: 612.5017 Evaluate side-chains 379 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 331 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 41 residues processed: 9 average time/residue: 0.5689 time to fit residues: 9.2187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 0.0570 chunk 23 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 348 GLN B 498 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1544 ASN B1596 GLN C 541 ASN C 642 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105028 restraints weight = 23173.439| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.93 r_work: 0.3168 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 17384 Z= 0.169 Angle : 0.569 12.880 23673 Z= 0.293 Chirality : 0.040 0.189 2563 Planarity : 0.005 0.063 2873 Dihedral : 11.389 175.110 2709 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 1951 helix: 1.85 (0.20), residues: 705 sheet: 0.63 (0.31), residues: 255 loop : -1.49 (0.17), residues: 991 =============================================================================== Job complete usr+sys time: 8598.52 seconds wall clock time: 151 minutes 49.73 seconds (9109.73 seconds total)