Starting phenix.real_space_refine (version: dev) on Mon Feb 20 14:38:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2023/7y82_33678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2023/7y82_33678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2023/7y82_33678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2023/7y82_33678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2023/7y82_33678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2023/7y82_33678.pdb" } resolution = 2.83 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= 0.057 sd= 0.202 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 Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A PHE 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1437": "OE1" <-> "OE2" Residue "A GLU 1474": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12278 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10869 Classifications: {'peptide': 1341} Link IDs: {'PTRANS': 60, 'TRANS': 1280} Chain breaks: 11 Chain: "B" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 859 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 12, 'rna3p_pur': 6, 'rna3p_pyr': 13} Link IDs: {'rna2p': 22, 'rna3p': 18} Chain: "C" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 16, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 21} 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 5559 SG CYS A 750 17.233 87.403 77.675 1.00 50.13 S ATOM 5572 SG CYS A 752 20.486 88.307 79.395 1.00 49.51 S ATOM 5594 SG CYS A 755 20.281 85.074 77.449 1.00 47.65 S ATOM 3484 SG CYS A 491 24.772 83.200 49.469 1.00 51.27 S ATOM 3566 SG CYS A 503 27.798 84.005 47.660 1.00 55.13 S ATOM 3588 SG CYS A 506 27.428 81.206 47.799 1.00 45.08 S ATOM 7485 SG CYS A1018 20.713 71.392 110.954 1.00 16.20 S ATOM 8652 SG CYS A1406 18.439 72.617 108.245 1.00 14.54 S ATOM 8703 SG CYS A1414 20.462 75.050 110.441 1.00 27.52 S ATOM 8720 SG CYS A1417 22.268 73.059 107.858 1.00 31.73 S ATOM 668 SG CYS A 88 30.731 71.787 18.806 1.00 53.90 S ATOM 939 SG CYS A 121 31.101 69.654 15.642 1.00 66.45 S ATOM 985 SG CYS A 127 33.362 69.126 18.711 1.00 55.44 S ATOM 1009 SG CYS A 130 29.754 68.099 18.835 1.00 56.81 S Time building chain proxies: 7.43, per 1000 atoms: 0.61 Number of scatterers: 12278 At special positions: 0 Unit cell: (72.6, 110, 157.3, 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 33 16.00 P 66 15.00 Mg 1 11.99 O 2478 8.00 N 2147 7.00 C 7549 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: 5.99 Conformation dependent library (CDL) restraints added in 1.6 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 755 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 750 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1414 " 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 127 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 121 " Number of angles added : 15 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 21 sheets defined 35.4% alpha, 23.9% beta 22 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.122A 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 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' 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 removed outlier: 3.555A pdb=" N ASP A 148 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 149 " --> pdb=" O ASN A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 149' Processing helix chain 'A' and resid 168 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: 3.746A pdb=" N ALA A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.992A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 354 through 374 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.605A 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 594 through 598 Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.514A pdb=" N TYR A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.545A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 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: 3.652A 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 1177 through 1201 Processing helix chain 'A' and resid 1201 through 1211 Processing helix chain 'A' and resid 1327 through 1340 Processing helix chain 'A' and resid 1346 through 1354 removed outlier: 4.373A pdb=" N ARG A1352 " --> pdb=" O GLU A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1400 through 1404 Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.799A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.529A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) 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 removed outlier: 3.847A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for '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 sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.671A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA A 53 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.941A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 153 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: 6.349A 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 333 through 334 Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 4.976A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 4.976A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.282A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 534 removed outlier: 10.184A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 11.035A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 539 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.487A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.487A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.197A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 791 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N LYS A 802 " --> pdb=" O HIS A 789 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N HIS A 789 " --> pdb=" O LYS A 802 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N LYS A 804 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 11.633A pdb=" N ILE A 787 " --> pdb=" O LYS A 804 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB6, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AB7, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB8, first strand: chain 'A' and resid 991 through 992 removed outlier: 3.513A pdb=" N GLU A 995 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1436 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA A1434 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASP A1521 " --> pdb=" O ALA A1434 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR A1436 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER A1519 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A1438 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 6.647A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.464A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLU A1510 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR A 987 " --> pdb=" O GLU A1510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1029 through 1031 Processing sheet with id=AC3, first strand: chain 'A' and resid 1369 through 1371 removed outlier: 3.604A pdb=" N SER A1380 " --> pdb=" O HIS A1371 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 6.14 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: 2168 1.33 - 1.45: 3601 1.45 - 1.57: 6741 1.57 - 1.69: 130 1.69 - 1.81: 45 Bond restraints: 12685 Sorted by residual: bond pdb=" C ARG A 719 " pdb=" O ARG A 719 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.24e-02 6.50e+03 6.24e+00 bond pdb=" C PRO A 718 " pdb=" O PRO A 718 " ideal model delta sigma weight residual 1.233 1.204 0.029 1.19e-02 7.06e+03 6.06e+00 bond pdb=" C PRO A 716 " pdb=" O PRO A 716 " ideal model delta sigma weight residual 1.237 1.207 0.030 1.26e-02 6.30e+03 5.75e+00 bond pdb=" N PRO A 716 " pdb=" CA PRO A 716 " ideal model delta sigma weight residual 1.472 1.449 0.023 1.32e-02 5.74e+03 2.93e+00 bond pdb=" N GLU A 717 " pdb=" CA GLU A 717 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.60e-02 3.91e+03 2.87e+00 ... (remaining 12680 not shown) Histogram of bond angle deviations from ideal: 96.82 - 104.26: 382 104.26 - 111.71: 6008 111.71 - 119.16: 4387 119.16 - 126.61: 6282 126.61 - 134.05: 355 Bond angle restraints: 17414 Sorted by residual: angle pdb=" O4' G B 47 " pdb=" C1' G B 47 " pdb=" N9 G B 47 " ideal model delta sigma weight residual 108.20 115.99 -7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" O4' A B 35 " pdb=" C1' A B 35 " pdb=" N9 A B 35 " ideal model delta sigma weight residual 108.20 115.66 -7.46 1.50e+00 4.44e-01 2.47e+01 angle pdb=" N PRO A 648 " pdb=" CD PRO A 648 " pdb=" CG PRO A 648 " ideal model delta sigma weight residual 103.20 96.82 6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" CA PRO A 648 " pdb=" N PRO A 648 " pdb=" CD PRO A 648 " ideal model delta sigma weight residual 112.00 106.42 5.58 1.40e+00 5.10e-01 1.59e+01 angle pdb=" C GLU A 717 " pdb=" CA GLU A 717 " pdb=" CB GLU A 717 " ideal model delta sigma weight residual 109.85 113.47 -3.62 1.14e+00 7.69e-01 1.01e+01 ... (remaining 17409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 7004 32.94 - 65.89: 409 65.89 - 98.83: 36 98.83 - 131.77: 3 131.77 - 164.72: 1 Dihedral angle restraints: 7453 sinusoidal: 3614 harmonic: 3839 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 67.28 164.72 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" CA ASN A1689 " pdb=" C ASN A1689 " pdb=" N PRO A1690 " pdb=" CA PRO A1690 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PRO A1440 " pdb=" C PRO A1440 " pdb=" N GLU A1441 " pdb=" CA GLU A1441 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 7450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1759 0.079 - 0.158: 136 0.158 - 0.237: 3 0.237 - 0.316: 1 0.316 - 0.395: 2 Chirality restraints: 1901 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 2.04 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C1' A B 35 " pdb=" O4' A B 35 " pdb=" C2' A B 35 " pdb=" N9 A B 35 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CB ILE A1444 " pdb=" CA ILE A1444 " pdb=" CG1 ILE A1444 " pdb=" CG2 ILE A1444 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1898 not shown) Planarity restraints: 2003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 47 " 0.051 2.00e-02 2.50e+03 2.29e-02 1.58e+01 pdb=" N9 G B 47 " -0.059 2.00e-02 2.50e+03 pdb=" C8 G B 47 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 47 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 47 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 47 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G B 47 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G B 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 47 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G B 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 35 " 0.045 2.00e-02 2.50e+03 2.13e-02 1.24e+01 pdb=" N9 A B 35 " -0.052 2.00e-02 2.50e+03 pdb=" C8 A B 35 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B 35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B 35 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 35 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 35 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A B 35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 35 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A B 35 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 45 " 0.035 2.00e-02 2.50e+03 1.80e-02 7.32e+00 pdb=" N1 C B 45 " -0.038 2.00e-02 2.50e+03 pdb=" C2 C B 45 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C B 45 " -0.006 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 " 0.012 2.00e-02 2.50e+03 pdb=" C5 C B 45 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C B 45 " -0.006 2.00e-02 2.50e+03 ... (remaining 2000 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 127 2.49 - 3.09: 8549 3.09 - 3.69: 20912 3.69 - 4.30: 31507 4.30 - 4.90: 50559 Nonbonded interactions: 111654 Sorted by model distance: nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1804 " model vdw 1.887 2.170 nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1804 " model vdw 1.893 2.170 nonbonded pdb=" O GLY A 134 " pdb="MG MG A1804 " model vdw 2.000 2.170 nonbonded pdb=" O2 C B 38 " pdb=" N2 G C 16 " model vdw 2.093 2.496 nonbonded pdb=" O LYS A 189 " pdb=" O2' U C 19 " model vdw 2.099 2.440 ... (remaining 111649 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 66 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 7549 2.51 5 N 2147 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.010 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: 4.800 Check model and map are aligned: 0.190 Process input model: 43.320 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.003 0.059 12685 Z= 0.199 Angle : 0.566 9.140 17414 Z= 0.302 Chirality : 0.042 0.395 1901 Planarity : 0.004 0.104 2003 Dihedral : 18.573 164.716 4993 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 4.59 % 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: 0.77 (0.23), residues: 1317 helix: 1.63 (0.27), residues: 400 sheet: -0.53 (0.36), residues: 182 loop : 0.27 (0.23), residues: 735 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 1.437 Fit side-chains outliers start: 54 outliers final: 46 residues processed: 188 average time/residue: 1.0189 time to fit residues: 213.4330 Evaluate side-chains 177 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 131 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 45 residues processed: 1 average time/residue: 0.1397 time to fit residues: 2.2760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN A 913 GLN A 955 ASN ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN A1635 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12685 Z= 0.204 Angle : 0.528 7.577 17414 Z= 0.278 Chirality : 0.042 0.392 1901 Planarity : 0.004 0.044 2003 Dihedral : 13.495 164.789 2245 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 6.55 % 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: 0.87 (0.23), residues: 1317 helix: 1.88 (0.26), residues: 400 sheet: -0.54 (0.35), residues: 197 loop : 0.27 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 142 time to evaluate : 1.458 Fit side-chains outliers start: 77 outliers final: 50 residues processed: 206 average time/residue: 1.0897 time to fit residues: 248.5909 Evaluate side-chains 183 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 133 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 43 residues processed: 7 average time/residue: 0.7900 time to fit residues: 8.2394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.0020 chunk 105 optimal weight: 0.0170 chunk 86 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.9228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 913 GLN A 955 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN A1584 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 12685 Z= 0.231 Angle : 0.523 7.559 17414 Z= 0.276 Chirality : 0.042 0.388 1901 Planarity : 0.004 0.046 2003 Dihedral : 13.502 165.045 2245 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 7.06 % 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: 0.85 (0.23), residues: 1317 helix: 1.84 (0.26), residues: 406 sheet: -0.65 (0.34), residues: 202 loop : 0.29 (0.23), residues: 709 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 143 time to evaluate : 1.368 Fit side-chains revert: symmetry clash outliers start: 83 outliers final: 52 residues processed: 210 average time/residue: 1.0557 time to fit residues: 246.1105 Evaluate side-chains 186 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 134 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 46 residues processed: 6 average time/residue: 0.5394 time to fit residues: 5.9170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 909 GLN A 913 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1584 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 12685 Z= 0.369 Angle : 0.580 8.412 17414 Z= 0.304 Chirality : 0.045 0.432 1901 Planarity : 0.004 0.044 2003 Dihedral : 13.499 161.388 2245 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 6.89 % 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: 0.66 (0.23), residues: 1317 helix: 1.67 (0.26), residues: 406 sheet: -0.64 (0.34), residues: 213 loop : 0.16 (0.23), residues: 698 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 137 time to evaluate : 1.295 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 57 residues processed: 204 average time/residue: 1.1017 time to fit residues: 248.4008 Evaluate side-chains 194 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 137 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 51 residues processed: 6 average time/residue: 0.5051 time to fit residues: 5.6291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 0.0030 chunk 0 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1584 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12685 Z= 0.190 Angle : 0.524 7.673 17414 Z= 0.276 Chirality : 0.042 0.392 1901 Planarity : 0.004 0.042 2003 Dihedral : 13.536 164.451 2245 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 6.12 % 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: 0.85 (0.23), residues: 1317 helix: 1.91 (0.26), residues: 407 sheet: -0.60 (0.34), residues: 213 loop : 0.25 (0.24), residues: 697 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 138 time to evaluate : 1.418 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 55 residues processed: 196 average time/residue: 1.0716 time to fit residues: 232.9598 Evaluate side-chains 187 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 132 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 48 residues processed: 7 average time/residue: 0.4342 time to fit residues: 5.4707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.0060 chunk 130 optimal weight: 5.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN A 913 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 12685 Z= 0.277 Angle : 0.546 9.023 17414 Z= 0.285 Chirality : 0.043 0.392 1901 Planarity : 0.004 0.041 2003 Dihedral : 13.527 163.403 2245 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 6.04 % 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: 0.77 (0.23), residues: 1317 helix: 1.84 (0.26), residues: 413 sheet: -0.64 (0.34), residues: 213 loop : 0.19 (0.24), residues: 691 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 138 time to evaluate : 1.461 Fit side-chains revert: symmetry clash outliers start: 71 outliers final: 54 residues processed: 196 average time/residue: 0.9889 time to fit residues: 216.0047 Evaluate side-chains 185 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 131 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 47 residues processed: 7 average time/residue: 0.1263 time to fit residues: 3.3352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 84 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 913 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12685 Z= 0.212 Angle : 0.529 9.986 17414 Z= 0.276 Chirality : 0.042 0.386 1901 Planarity : 0.004 0.040 2003 Dihedral : 13.554 164.654 2245 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 6.21 % 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: 0.84 (0.23), residues: 1317 helix: 1.91 (0.26), residues: 413 sheet: -0.65 (0.34), residues: 213 loop : 0.23 (0.24), residues: 691 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 134 time to evaluate : 1.559 Fit side-chains revert: symmetry clash outliers start: 73 outliers final: 54 residues processed: 192 average time/residue: 1.0852 time to fit residues: 231.0521 Evaluate side-chains 178 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 124 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 47 residues processed: 7 average time/residue: 0.5088 time to fit residues: 6.2324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN A 913 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1584 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 12685 Z= 0.303 Angle : 0.560 9.929 17414 Z= 0.292 Chirality : 0.043 0.401 1901 Planarity : 0.004 0.043 2003 Dihedral : 13.560 162.445 2245 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 5.44 % 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: 0.75 (0.23), residues: 1317 helix: 1.80 (0.26), residues: 413 sheet: -0.70 (0.34), residues: 213 loop : 0.20 (0.24), residues: 691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 131 time to evaluate : 1.389 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 54 residues processed: 185 average time/residue: 1.0676 time to fit residues: 219.4704 Evaluate side-chains 184 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 130 time to evaluate : 1.446 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 47 residues processed: 7 average time/residue: 0.1482 time to fit residues: 3.7916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 913 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 12685 Z= 0.253 Angle : 0.551 9.721 17414 Z= 0.286 Chirality : 0.042 0.379 1901 Planarity : 0.004 0.043 2003 Dihedral : 13.576 162.484 2245 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 4.85 % 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: 0.76 (0.23), residues: 1317 helix: 1.81 (0.26), residues: 413 sheet: -0.75 (0.34), residues: 213 loop : 0.23 (0.24), residues: 691 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 132 time to evaluate : 1.455 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 50 residues processed: 183 average time/residue: 1.1003 time to fit residues: 223.9422 Evaluate side-chains 180 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 130 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 46 residues processed: 4 average time/residue: 0.1418 time to fit residues: 2.8370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN A 913 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1584 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 12685 Z= 0.340 Angle : 0.589 9.755 17414 Z= 0.305 Chirality : 0.044 0.428 1901 Planarity : 0.004 0.050 2003 Dihedral : 13.579 159.815 2245 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 4.59 % 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: 0.64 (0.23), residues: 1317 helix: 1.68 (0.26), residues: 413 sheet: -0.84 (0.34), residues: 213 loop : 0.19 (0.24), residues: 691 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 135 time to evaluate : 1.369 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 48 residues processed: 181 average time/residue: 1.0552 time to fit residues: 212.7955 Evaluate side-chains 180 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 132 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 4 average time/residue: 0.1464 time to fit residues: 2.9181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 114 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1584 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.154104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113981 restraints weight = 15185.605| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.85 r_work: 0.3314 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12685 Z= 0.191 Angle : 0.542 9.651 17414 Z= 0.282 Chirality : 0.042 0.387 1901 Planarity : 0.004 0.048 2003 Dihedral : 13.599 164.038 2245 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 4.68 % 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: 0.90 (0.23), residues: 1317 helix: 1.98 (0.26), residues: 407 sheet: -0.72 (0.34), residues: 213 loop : 0.31 (0.24), residues: 697 =============================================================================== Job complete usr+sys time: 4468.26 seconds wall clock time: 81 minutes 12.69 seconds (4872.69 seconds total)