Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 03:41:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y85_33681/04_2023/7y85_33681.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y85_33681/04_2023/7y85_33681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y85_33681/04_2023/7y85_33681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y85_33681/04_2023/7y85_33681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y85_33681/04_2023/7y85_33681.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y85_33681/04_2023/7y85_33681.pdb" } resolution = 2.73 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= -0.001 sd= 0.218 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 59 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 10284 2.51 5 N 2862 2.21 5 O 3236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A GLU 959": "OE1" <-> "OE2" Residue "A GLU 1504": "OE1" <-> "OE2" Residue "A GLU 1529": "OE1" <-> "OE2" Residue "A GLU 1589": "OE1" <-> "OE2" Residue "A GLU 1600": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D GLU 587": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16502 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1232, 9941 Classifications: {'peptide': 1232} Link IDs: {'PTRANS': 58, 'TRANS': 1173} Chain breaks: 9 Chain: "B" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 757 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "C" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 496 Classifications: {'RNA': 23} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 14, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 19} Chain: "D" Number of atoms: 5303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5303 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 18, 'TRANS': 633} Chain breaks: 6 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 1, ' ZN': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5602 SG CYS A 750 47.049 32.564 71.788 1.00 94.79 S ATOM 5615 SG CYS A 752 44.045 33.881 73.684 1.00 81.51 S ATOM 5637 SG CYS A 755 46.744 36.305 72.550 1.00 83.83 S ATOM 3527 SG CYS A 491 48.404 50.205 48.362 1.00 96.92 S ATOM 3595 SG CYS A 501 48.817 50.090 44.835 1.00 81.08 S ATOM 3609 SG CYS A 503 45.580 51.529 46.224 1.00 80.61 S ATOM 3631 SG CYS A 506 48.792 53.564 46.794 1.00 77.65 S ATOM 7528 SG CYS A1018 52.973 34.547 108.275 1.00 92.82 S ATOM 7724 SG CYS A1406 53.817 32.771 105.027 1.00 87.47 S ATOM 7775 SG CYS A1414 50.452 32.245 106.711 1.00 92.36 S ATOM 7792 SG CYS A1417 51.062 35.493 105.093 1.00 95.26 S ATOM 668 SG CYS A 88 56.259 69.552 22.627 1.00 86.53 S ATOM 939 SG CYS A 121 58.076 72.372 20.716 1.00 93.44 S ATOM 985 SG CYS A 127 56.652 72.986 24.153 1.00 80.77 S ATOM 1009 SG CYS A 130 59.592 70.552 23.731 1.00 70.98 S Time building chain proxies: 8.61, per 1000 atoms: 0.52 Number of scatterers: 16502 At special positions: 0 Unit cell: (100.1, 96.8, 158.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 56 16.00 P 59 15.00 Mg 1 11.99 O 3236 8.00 N 2862 7.00 C 10284 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: 7.02 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 755 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1406 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 121 " Number of angles added : 21 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3488 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 23 sheets defined 42.5% alpha, 19.6% beta 14 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 5.80 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.069A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.564A pdb=" N GLY A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 290 through 307 removed outlier: 4.248A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N HIS A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.647A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.591A pdb=" N LEU A 642 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 665 removed outlier: 3.515A pdb=" N GLU A 663 " --> pdb=" O PHE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.689A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.503A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 744 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.557A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.240A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 Processing helix chain 'A' and resid 1493 through 1501 Processing helix chain 'A' and resid 1528 through 1540 Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1603 Processing helix chain 'A' and resid 1615 through 1618 Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1668 Processing helix chain 'A' and resid 1673 through 1683 Processing helix chain 'D' and resid 16 through 33 removed outlier: 4.240A pdb=" N ARG D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 60 removed outlier: 3.721A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 64 through 81 removed outlier: 3.875A pdb=" N ALA D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 80 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 109 removed outlier: 3.508A pdb=" N PHE D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 136 Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.832A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.685A pdb=" N LEU D 187 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 188 " --> pdb=" O PHE D 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 188' Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 210 through 223 removed outlier: 4.348A pdb=" N GLU D 214 " --> pdb=" O HIS D 210 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.772A pdb=" N ASP D 234 " --> pdb=" O HIS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.525A pdb=" N ILE D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 296 removed outlier: 4.325A pdb=" N ARG D 282 " --> pdb=" O TRP D 278 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 323 removed outlier: 3.819A pdb=" N ILE D 310 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.785A pdb=" N LYS D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 361 removed outlier: 4.446A pdb=" N TYR D 360 " --> pdb=" O TYR D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 451 removed outlier: 4.180A pdb=" N LEU D 436 " --> pdb=" O GLN D 432 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 469 removed outlier: 3.503A pdb=" N THR D 460 " --> pdb=" O GLU D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 473 Processing helix chain 'D' and resid 489 through 494 Processing helix chain 'D' and resid 509 through 514 removed outlier: 4.048A pdb=" N ASN D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 543 through 547 Processing helix chain 'D' and resid 566 through 573 removed outlier: 3.561A pdb=" N GLU D 571 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 607 through 614 Processing helix chain 'D' and resid 627 through 632 Processing helix chain 'D' and resid 644 through 652 removed outlier: 3.656A pdb=" N ALA D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 679 removed outlier: 3.681A pdb=" N THR D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN D 679 " --> pdb=" O TRP D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 691 removed outlier: 3.892A pdb=" N TRP D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 708 removed outlier: 3.722A pdb=" N PHE D 703 " --> pdb=" O HIS D 699 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.718A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.985A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR A 191 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 178 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG A 193 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 176 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TRP A 195 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER A 174 " --> pdb=" O TRP A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.749A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 5.841A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.453A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.453A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.134A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 533 removed outlier: 10.325A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.519A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.519A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.088A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ALA A 803 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB5, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AB6, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.272A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA A1434 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ASP A1521 " --> pdb=" O ALA A1434 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR A1436 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER A1519 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A1438 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 6.860A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A1567 " --> pdb=" O VAL A1582 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.439A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 989 " --> pdb=" O GLU A1510 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AC2, first strand: chain 'D' and resid 274 through 276 removed outlier: 6.587A pdb=" N ARG D 275 " --> pdb=" O LEU D 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 425 through 431 Processing sheet with id=AC4, first strand: chain 'D' and resid 536 through 540 removed outlier: 6.180A pdb=" N LEU D 580 " --> pdb=" O ILE D 623 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL D 622 " --> pdb=" O VAL D 658 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR D 660 " --> pdb=" O VAL D 622 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU D 624 " --> pdb=" O THR D 660 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 586 through 587 649 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 7.47 Time building geometry restraints manager: 7.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2831 1.32 - 1.45: 4756 1.45 - 1.57: 9203 1.57 - 1.69: 116 1.69 - 1.82: 78 Bond restraints: 16984 Sorted by residual: bond pdb=" O3' C B 45 " pdb=" P U B 46 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.50e-02 4.44e+03 2.16e+01 bond pdb=" C PRO A 911 " pdb=" O PRO A 911 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.26e-02 6.30e+03 9.57e+00 bond pdb=" N SER A 910 " pdb=" CA SER A 910 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.41e+00 bond pdb=" C PRO A1614 " pdb=" O PRO A1614 " ideal model delta sigma weight residual 1.233 1.206 0.028 1.06e-02 8.90e+03 6.83e+00 bond pdb=" P U B 46 " pdb=" OP2 U B 46 " ideal model delta sigma weight residual 1.485 1.437 0.048 2.00e-02 2.50e+03 5.85e+00 ... (remaining 16979 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.44: 530 105.44 - 112.59: 8867 112.59 - 119.74: 5632 119.74 - 126.89: 7780 126.89 - 134.04: 361 Bond angle restraints: 23170 Sorted by residual: angle pdb=" C3' C B 45 " pdb=" O3' C B 45 " pdb=" P U B 46 " ideal model delta sigma weight residual 120.20 111.64 8.56 1.50e+00 4.44e-01 3.26e+01 angle pdb=" O3' U B 46 " pdb=" C3' U B 46 " pdb=" C2' U B 46 " ideal model delta sigma weight residual 109.50 101.58 7.92 1.50e+00 4.44e-01 2.79e+01 angle pdb=" C ALA D 601 " pdb=" CA ALA D 601 " pdb=" CB ALA D 601 " ideal model delta sigma weight residual 117.23 110.17 7.06 1.36e+00 5.41e-01 2.69e+01 angle pdb=" O4' G B 47 " pdb=" C1' G B 47 " pdb=" N9 G B 47 " ideal model delta sigma weight residual 108.20 115.76 -7.56 1.50e+00 4.44e-01 2.54e+01 angle pdb=" C3' U B 46 " pdb=" C2' U B 46 " pdb=" O2' U B 46 " ideal model delta sigma weight residual 114.60 121.66 -7.06 1.50e+00 4.44e-01 2.22e+01 ... (remaining 23165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.70: 9493 34.70 - 69.41: 532 69.41 - 104.11: 30 104.11 - 138.81: 1 138.81 - 173.52: 1 Dihedral angle restraints: 10057 sinusoidal: 4636 harmonic: 5421 Sorted by residual: dihedral pdb=" O4' U C 14 " pdb=" C1' U C 14 " pdb=" N1 U C 14 " pdb=" C2 U C 14 " ideal model delta sinusoidal sigma weight residual 232.00 58.48 173.52 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA CYS A 491 " pdb=" C CYS A 491 " pdb=" N ASN A 492 " pdb=" CA ASN A 492 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" C4' U B 46 " pdb=" C3' U B 46 " pdb=" C2' U B 46 " pdb=" C1' U B 46 " ideal model delta sinusoidal sigma weight residual -35.00 -7.95 -27.05 1 8.00e+00 1.56e-02 1.64e+01 ... (remaining 10054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2321 0.074 - 0.147: 195 0.147 - 0.221: 6 0.221 - 0.294: 2 0.294 - 0.368: 2 Chirality restraints: 2526 Sorted by residual: chirality pdb=" C1' G B 47 " pdb=" O4' G B 47 " pdb=" C2' G B 47 " pdb=" N9 G B 47 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C2' U B 46 " pdb=" C3' U B 46 " pdb=" O2' U B 46 " pdb=" C1' U B 46 " both_signs ideal model delta sigma weight residual False -2.52 -2.17 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" P U B 46 " pdb=" OP1 U B 46 " pdb=" OP2 U B 46 " pdb=" O5' U B 46 " both_signs ideal model delta sigma weight residual True 2.41 -2.13 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2523 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 47 " 0.047 2.00e-02 2.50e+03 2.19e-02 1.44e+01 pdb=" N9 G B 47 " -0.057 2.00e-02 2.50e+03 pdb=" C8 G B 47 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G B 47 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 47 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G B 47 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 47 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G B 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G B 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G B 47 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 23 " 0.029 2.00e-02 2.50e+03 1.50e-02 5.09e+00 pdb=" N1 U B 23 " -0.033 2.00e-02 2.50e+03 pdb=" C2 U B 23 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U B 23 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U B 23 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 23 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U B 23 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B 23 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U B 23 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 45 " -0.029 2.00e-02 2.50e+03 1.49e-02 4.97e+00 pdb=" N1 C B 45 " 0.032 2.00e-02 2.50e+03 pdb=" C2 C B 45 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C B 45 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C B 45 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 45 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C B 45 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C B 45 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B 45 " 0.005 2.00e-02 2.50e+03 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 180 2.53 - 3.12: 12223 3.12 - 3.72: 28935 3.72 - 4.31: 42608 4.31 - 4.90: 68535 Nonbonded interactions: 152481 Sorted by model distance: nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1804 " model vdw 1.940 2.170 nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1804 " model vdw 1.959 2.170 nonbonded pdb=" O GLY A 134 " pdb="MG MG A1804 " model vdw 2.060 2.170 nonbonded pdb=" O LYS D 321 " pdb=" OH TYR D 643 " model vdw 2.136 2.440 nonbonded pdb=" O ASP A 801 " pdb=" O2' C C 7 " model vdw 2.150 2.440 ... (remaining 152476 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: 0.770 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: 0.030 Extract box with map and model: 5.290 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 53.040 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.004 0.106 16984 Z= 0.246 Angle : 0.567 9.212 23170 Z= 0.307 Chirality : 0.042 0.368 2526 Planarity : 0.004 0.047 2755 Dihedral : 18.767 173.518 6569 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 3.87 % 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 (0.19), residues: 1850 helix: 0.30 (0.20), residues: 660 sheet: -0.68 (0.28), residues: 268 loop : 0.09 (0.20), residues: 922 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 206 time to evaluate : 1.983 Fit side-chains outliers start: 64 outliers final: 55 residues processed: 266 average time/residue: 1.1194 time to fit residues: 338.2508 Evaluate side-chains 250 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 195 time to evaluate : 1.918 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 53 residues processed: 3 average time/residue: 0.2684 time to fit residues: 3.9696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 49 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 58 optimal weight: 0.0030 chunk 91 optimal weight: 0.7980 chunk 112 optimal weight: 0.0040 chunk 175 optimal weight: 10.0000 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A1584 GLN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN D 427 GLN D 432 GLN D 448 ASN D 621 GLN D 699 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 16984 Z= 0.172 Angle : 0.526 7.957 23170 Z= 0.279 Chirality : 0.041 0.376 2526 Planarity : 0.004 0.045 2755 Dihedral : 11.284 175.821 2738 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 6.59 % 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: 0.19 (0.19), residues: 1850 helix: 0.69 (0.19), residues: 701 sheet: -0.46 (0.29), residues: 256 loop : -0.00 (0.20), residues: 893 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 244 time to evaluate : 1.856 Fit side-chains outliers start: 109 outliers final: 51 residues processed: 332 average time/residue: 1.2081 time to fit residues: 451.4173 Evaluate side-chains 267 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 216 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 46 residues processed: 5 average time/residue: 0.1756 time to fit residues: 3.9133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1596 GLN D 133 ASN D 150 ASN D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 ASN D 621 GLN D 699 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.063 16984 Z= 0.489 Angle : 0.647 8.078 23170 Z= 0.339 Chirality : 0.047 0.346 2526 Planarity : 0.005 0.061 2755 Dihedral : 11.443 166.392 2738 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 7.20 % 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: -0.13 (0.19), residues: 1850 helix: 0.36 (0.19), residues: 702 sheet: -0.75 (0.28), residues: 271 loop : -0.07 (0.21), residues: 877 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 222 time to evaluate : 1.931 Fit side-chains outliers start: 119 outliers final: 71 residues processed: 317 average time/residue: 1.2427 time to fit residues: 444.6793 Evaluate side-chains 279 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 208 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 61 residues processed: 10 average time/residue: 0.4203 time to fit residues: 8.4101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 186 optimal weight: 0.0000 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A1492 GLN D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN D 699 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 16984 Z= 0.262 Angle : 0.555 8.268 23170 Z= 0.290 Chirality : 0.042 0.366 2526 Planarity : 0.004 0.050 2755 Dihedral : 11.359 170.040 2738 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 6.41 % 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: 0.08 (0.19), residues: 1850 helix: 0.61 (0.19), residues: 704 sheet: -0.65 (0.29), residues: 266 loop : -0.02 (0.21), residues: 880 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 216 time to evaluate : 2.069 Fit side-chains revert: symmetry clash outliers start: 106 outliers final: 67 residues processed: 302 average time/residue: 1.2111 time to fit residues: 412.3245 Evaluate side-chains 282 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 215 time to evaluate : 1.789 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 60 residues processed: 7 average time/residue: 0.1884 time to fit residues: 4.9519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 287 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN D 699 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 16984 Z= 0.456 Angle : 0.629 8.928 23170 Z= 0.328 Chirality : 0.046 0.352 2526 Planarity : 0.005 0.057 2755 Dihedral : 11.434 166.752 2738 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 6.47 % 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: -0.16 (0.19), residues: 1850 helix: 0.37 (0.19), residues: 708 sheet: -0.81 (0.29), residues: 271 loop : -0.10 (0.21), residues: 871 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 215 time to evaluate : 2.241 Fit side-chains outliers start: 107 outliers final: 74 residues processed: 305 average time/residue: 1.2265 time to fit residues: 420.7677 Evaluate side-chains 279 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 205 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 66 residues processed: 8 average time/residue: 0.5318 time to fit residues: 7.9541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 287 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A1492 GLN D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN D 699 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16984 Z= 0.198 Angle : 0.530 8.920 23170 Z= 0.278 Chirality : 0.041 0.372 2526 Planarity : 0.004 0.051 2755 Dihedral : 11.329 172.082 2738 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 5.51 % 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: 0.21 (0.19), residues: 1850 helix: 0.82 (0.19), residues: 697 sheet: -0.66 (0.30), residues: 257 loop : -0.02 (0.21), residues: 896 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 228 time to evaluate : 1.916 Fit side-chains outliers start: 91 outliers final: 62 residues processed: 309 average time/residue: 1.2425 time to fit residues: 431.6969 Evaluate side-chains 271 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 209 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 60 residues processed: 2 average time/residue: 0.2708 time to fit residues: 5.3770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 287 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN D 699 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 16984 Z= 0.405 Angle : 0.606 9.178 23170 Z= 0.315 Chirality : 0.045 0.357 2526 Planarity : 0.004 0.052 2755 Dihedral : 11.375 168.462 2738 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 5.51 % 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: -0.01 (0.19), residues: 1850 helix: 0.56 (0.19), residues: 703 sheet: -0.84 (0.29), residues: 270 loop : -0.03 (0.21), residues: 877 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 208 time to evaluate : 1.760 Fit side-chains outliers start: 91 outliers final: 67 residues processed: 287 average time/residue: 1.1880 time to fit residues: 386.0603 Evaluate side-chains 271 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 204 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 64 residues processed: 3 average time/residue: 0.2286 time to fit residues: 3.8072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1592 ASN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN D 699 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16984 Z= 0.212 Angle : 0.536 9.282 23170 Z= 0.280 Chirality : 0.041 0.375 2526 Planarity : 0.004 0.052 2755 Dihedral : 11.320 172.353 2738 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 5.26 % 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: 0.28 (0.19), residues: 1850 helix: 0.86 (0.19), residues: 694 sheet: -0.58 (0.30), residues: 263 loop : 0.03 (0.21), residues: 893 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 213 time to evaluate : 2.038 Fit side-chains outliers start: 87 outliers final: 64 residues processed: 290 average time/residue: 1.1994 time to fit residues: 394.4119 Evaluate side-chains 270 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 206 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 59 residues processed: 5 average time/residue: 0.2152 time to fit residues: 4.6078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1592 ASN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN D 699 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 16984 Z= 0.271 Angle : 0.557 9.350 23170 Z= 0.290 Chirality : 0.042 0.369 2526 Planarity : 0.004 0.052 2755 Dihedral : 11.293 171.550 2738 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 4.23 % 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: 0.16 (0.19), residues: 1850 helix: 0.75 (0.19), residues: 712 sheet: -0.72 (0.30), residues: 267 loop : -0.01 (0.22), residues: 871 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 208 time to evaluate : 1.778 Fit side-chains outliers start: 70 outliers final: 62 residues processed: 274 average time/residue: 1.1651 time to fit residues: 361.7783 Evaluate side-chains 264 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 202 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 60 residues processed: 3 average time/residue: 0.5620 time to fit residues: 4.7500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN D 699 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 16984 Z= 0.297 Angle : 0.576 9.570 23170 Z= 0.300 Chirality : 0.043 0.367 2526 Planarity : 0.004 0.053 2755 Dihedral : 11.308 170.825 2738 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 3.93 % 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: 0.12 (0.19), residues: 1850 helix: 0.71 (0.19), residues: 712 sheet: -0.75 (0.30), residues: 267 loop : -0.03 (0.21), residues: 871 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 205 time to evaluate : 2.074 Fit side-chains outliers start: 65 outliers final: 60 residues processed: 268 average time/residue: 1.1961 time to fit residues: 363.9340 Evaluate side-chains 262 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 202 time to evaluate : 2.087 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 60 residues processed: 1 average time/residue: 0.3160 time to fit residues: 3.2911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN D 699 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114702 restraints weight = 17340.961| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.72 r_work: 0.3196 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 16984 Z= 0.293 Angle : 0.574 9.757 23170 Z= 0.299 Chirality : 0.043 0.367 2526 Planarity : 0.004 0.053 2755 Dihedral : 11.302 170.843 2738 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 4.30 % 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 (0.19), residues: 1850 helix: 0.69 (0.19), residues: 712 sheet: -0.67 (0.30), residues: 257 loop : -0.07 (0.21), residues: 881 =============================================================================== Job complete usr+sys time: 6516.78 seconds wall clock time: 116 minutes 57.33 seconds (7017.33 seconds total)