Starting phenix.real_space_refine on Thu Feb 15 12:52:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2024/7y82_33678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2024/7y82_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_2024/7y82_33678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2024/7y82_33678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2024/7y82_33678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y82_33678/02_2024/7y82_33678.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.057 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.29, per 1000 atoms: 0.59 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: 5.95 Conformation dependent library (CDL) restraints added in 2.1 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: 5.04 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: 6.14 Time building geometry restraints manager: 6.22 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: 7115 32.94 - 65.89: 521 65.89 - 98.83: 53 98.83 - 131.77: 3 131.77 - 164.72: 1 Dihedral angle restraints: 7693 sinusoidal: 3854 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 7690 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 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: 1.030 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: 4.200 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 45.000 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 20.346 164.716 5233 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 % Allowed : 26.70 % Favored : 68.71 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 82 HIS 0.012 0.001 HIS A 215 PHE 0.014 0.001 PHE A 546 TYR 0.017 0.001 TYR A 903 ARG 0.009 0.001 ARG A 846 *********************** 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 : 1.385 Fit side-chains REVERT: A 624 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: A 1619 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7121 (mp) outliers start: 54 outliers final: 46 residues processed: 188 average time/residue: 0.9994 time to fit residues: 209.3715 Evaluate side-chains 179 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 131 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1355 THR Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1453 SER Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1662 THR 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: 5.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- 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: 0.7848 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12685 Z= 0.248 Angle : 0.540 7.534 17414 Z= 0.285 Chirality : 0.043 0.389 1901 Planarity : 0.004 0.044 2003 Dihedral : 18.701 163.147 2563 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.42 % Allowed : 24.32 % Favored : 71.26 % 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: 0.80 (0.23), residues: 1317 helix: 1.77 (0.26), residues: 406 sheet: -0.53 (0.34), residues: 202 loop : 0.23 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 82 HIS 0.008 0.001 HIS A 215 PHE 0.013 0.001 PHE A1520 TYR 0.013 0.001 TYR A 903 ARG 0.006 0.000 ARG A 846 *********************** 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 193 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 141 time to evaluate : 1.393 Fit side-chains outliers start: 52 outliers final: 27 residues processed: 183 average time/residue: 1.0945 time to fit residues: 220.9406 Evaluate side-chains 162 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1453 SER Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR 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: 0.6980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 286 GLN 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0833 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= 0.223 Angle : 0.522 7.607 17414 Z= 0.275 Chirality : 0.042 0.394 1901 Planarity : 0.004 0.042 2003 Dihedral : 18.418 163.919 2511 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.76 % Allowed : 24.83 % Favored : 70.41 % 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: 0.90 (0.23), residues: 1317 helix: 1.85 (0.26), residues: 406 sheet: -0.49 (0.34), residues: 202 loop : 0.30 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 82 HIS 0.005 0.001 HIS A 215 PHE 0.013 0.001 PHE A 805 TYR 0.013 0.001 TYR A 903 ARG 0.008 0.000 ARG A 846 *********************** 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 197 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 141 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 566 HIS cc_start: 0.7430 (m-70) cc_final: 0.7198 (m-70) REVERT: A 618 ILE cc_start: 0.8280 (tp) cc_final: 0.7972 (mt) REVERT: A 624 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6568 (tp30) REVERT: A 662 LYS cc_start: 0.7516 (mtmm) cc_final: 0.7064 (mtmt) REVERT: A 1197 ILE cc_start: 0.6385 (OUTLIER) cc_final: 0.6183 (mp) outliers start: 56 outliers final: 25 residues processed: 182 average time/residue: 1.1799 time to fit residues: 235.6377 Evaluate side-chains 154 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN A 909 GLN 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 A1584 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12685 Z= 0.395 Angle : 0.591 8.782 17414 Z= 0.309 Chirality : 0.045 0.463 1901 Planarity : 0.004 0.041 2003 Dihedral : 18.393 159.893 2502 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.53 % Allowed : 24.83 % Favored : 69.64 % 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: 0.65 (0.23), residues: 1317 helix: 1.62 (0.26), residues: 406 sheet: -0.72 (0.34), residues: 217 loop : 0.22 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 82 HIS 0.005 0.001 HIS A 215 PHE 0.017 0.002 PHE A 659 TYR 0.014 0.002 TYR A 903 ARG 0.007 0.001 ARG A 846 *********************** 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 205 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 140 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7989 (tp) REVERT: A 618 ILE cc_start: 0.8247 (tp) cc_final: 0.7932 (mt) REVERT: A 624 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6649 (tp30) outliers start: 65 outliers final: 36 residues processed: 185 average time/residue: 1.1960 time to fit residues: 242.5338 Evaluate side-chains 173 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1502 GLN Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 913 GLN A 955 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12685 Z= 0.197 Angle : 0.529 7.643 17414 Z= 0.279 Chirality : 0.042 0.392 1901 Planarity : 0.004 0.038 2003 Dihedral : 18.386 162.650 2502 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.42 % Allowed : 25.68 % Favored : 69.90 % 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: 1.88 (0.26), residues: 407 sheet: -0.62 (0.34), residues: 213 loop : 0.27 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 82 HIS 0.006 0.001 HIS A 215 PHE 0.017 0.001 PHE A 659 TYR 0.010 0.001 TYR A 903 ARG 0.007 0.000 ARG A 846 *********************** 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 189 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7857 (tp) REVERT: A 607 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7701 (tt) REVERT: A 618 ILE cc_start: 0.8167 (tp) cc_final: 0.7894 (mt) REVERT: A 624 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6592 (tp30) REVERT: A 662 LYS cc_start: 0.7548 (mtmm) cc_final: 0.7036 (mtmt) outliers start: 52 outliers final: 31 residues processed: 178 average time/residue: 1.2140 time to fit residues: 237.0015 Evaluate side-chains 164 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1502 GLN Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 0.0470 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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 A1502 GLN A1584 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1188 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= 0.213 Angle : 0.524 7.620 17414 Z= 0.276 Chirality : 0.042 0.390 1901 Planarity : 0.004 0.040 2003 Dihedral : 18.338 164.263 2502 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.42 % Allowed : 25.77 % Favored : 69.81 % 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: 0.86 (0.23), residues: 1317 helix: 1.93 (0.26), residues: 413 sheet: -0.61 (0.34), residues: 213 loop : 0.24 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 82 HIS 0.008 0.001 HIS A 215 PHE 0.016 0.001 PHE A 659 TYR 0.011 0.001 TYR A 903 ARG 0.006 0.000 ARG A 846 *********************** 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 191 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 139 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 607 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7704 (tt) REVERT: A 618 ILE cc_start: 0.8232 (tp) cc_final: 0.7976 (mt) REVERT: A 662 LYS cc_start: 0.7505 (mtmm) cc_final: 0.7039 (mtmt) REVERT: A 1417 CYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7757 (m) outliers start: 52 outliers final: 34 residues processed: 176 average time/residue: 1.1099 time to fit residues: 215.8450 Evaluate side-chains 165 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1417 CYS Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 913 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12685 Z= 0.213 Angle : 0.529 10.228 17414 Z= 0.276 Chirality : 0.042 0.391 1901 Planarity : 0.004 0.042 2003 Dihedral : 18.318 165.018 2502 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.85 % Allowed : 25.60 % Favored : 69.56 % 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: 0.93 (0.23), residues: 1317 helix: 2.00 (0.26), residues: 407 sheet: -0.62 (0.34), residues: 213 loop : 0.30 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 82 HIS 0.008 0.001 HIS A 215 PHE 0.016 0.001 PHE A 659 TYR 0.011 0.001 TYR A 903 ARG 0.007 0.000 ARG A 846 *********************** 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 193 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 136 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7830 (tp) REVERT: A 607 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7636 (tt) REVERT: A 618 ILE cc_start: 0.8126 (tp) cc_final: 0.7915 (mt) REVERT: A 624 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6524 (tp30) REVERT: A 628 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.5101 (mtp180) REVERT: A 637 MET cc_start: 0.6791 (ptt) cc_final: 0.6440 (ptt) REVERT: A 662 LYS cc_start: 0.7491 (mtmm) cc_final: 0.7045 (mtmt) REVERT: A 1417 CYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7769 (m) outliers start: 57 outliers final: 31 residues processed: 177 average time/residue: 1.0742 time to fit residues: 209.3855 Evaluate side-chains 164 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1417 CYS Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1453 SER Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR 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: 4.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12685 Z= 0.375 Angle : 0.594 10.567 17414 Z= 0.308 Chirality : 0.045 0.473 1901 Planarity : 0.004 0.048 2003 Dihedral : 18.328 159.874 2496 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.34 % Allowed : 26.36 % Favored : 69.30 % 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: 0.68 (0.23), residues: 1317 helix: 1.76 (0.26), residues: 406 sheet: -0.81 (0.34), residues: 217 loop : 0.20 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 82 HIS 0.011 0.001 HIS A 215 PHE 0.018 0.002 PHE A 659 TYR 0.015 0.002 TYR A 903 ARG 0.007 0.001 ARG A1446 *********************** 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 180 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 129 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7889 (tp) REVERT: A 607 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7631 (tt) REVERT: A 618 ILE cc_start: 0.8069 (tp) cc_final: 0.7833 (mt) REVERT: A 624 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6606 (tp30) REVERT: A 628 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.5253 (mtp180) REVERT: A 659 PHE cc_start: 0.6845 (t80) cc_final: 0.6631 (t80) REVERT: A 662 LYS cc_start: 0.7533 (mtmm) cc_final: 0.7179 (mtmt) REVERT: A 1417 CYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7796 (m) outliers start: 51 outliers final: 33 residues processed: 165 average time/residue: 1.1399 time to fit residues: 207.9841 Evaluate side-chains 169 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1417 CYS Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1453 SER Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12685 Z= 0.194 Angle : 0.534 10.292 17414 Z= 0.280 Chirality : 0.042 0.401 1901 Planarity : 0.004 0.046 2003 Dihedral : 18.304 163.482 2496 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.57 % Allowed : 27.55 % Favored : 68.88 % 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: 0.89 (0.23), residues: 1317 helix: 1.98 (0.26), residues: 407 sheet: -0.71 (0.34), residues: 213 loop : 0.30 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 82 HIS 0.013 0.001 HIS A 215 PHE 0.016 0.001 PHE A 659 TYR 0.012 0.001 TYR A 903 ARG 0.009 0.001 ARG A1446 *********************** 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 172 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7826 (tp) REVERT: A 607 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7653 (tt) REVERT: A 624 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6508 (tp30) REVERT: A 662 LYS cc_start: 0.7442 (mtmm) cc_final: 0.7103 (mtmt) REVERT: A 1417 CYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7758 (m) outliers start: 42 outliers final: 27 residues processed: 162 average time/residue: 1.1497 time to fit residues: 205.2448 Evaluate side-chains 160 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1417 CYS Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1453 SER Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 0.0570 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 0.1980 chunk 118 optimal weight: 0.9980 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 A1502 GLN A1584 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12685 Z= 0.197 Angle : 0.532 9.539 17414 Z= 0.278 Chirality : 0.041 0.394 1901 Planarity : 0.004 0.046 2003 Dihedral : 18.244 165.367 2492 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.98 % Allowed : 28.57 % Favored : 68.45 % 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: 0.95 (0.23), residues: 1317 helix: 2.07 (0.26), residues: 407 sheet: -0.71 (0.34), residues: 213 loop : 0.31 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 82 HIS 0.013 0.001 HIS A 215 PHE 0.016 0.001 PHE A 659 TYR 0.012 0.001 TYR A 903 ARG 0.009 0.000 ARG A1446 ********************** 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 169 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 206 THR cc_start: 0.8506 (m) cc_final: 0.8245 (m) REVERT: A 624 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6450 (tp30) REVERT: A 662 LYS cc_start: 0.7516 (mtmm) cc_final: 0.7112 (mtmt) REVERT: A 1417 CYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7749 (m) outliers start: 35 outliers final: 26 residues processed: 157 average time/residue: 1.2139 time to fit residues: 209.3765 Evaluate side-chains 160 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1417 CYS Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1453 SER Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 114 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 913 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.154233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113910 restraints weight = 15162.287| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.87 r_work: 0.3306 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12685 Z= 0.206 Angle : 0.536 9.725 17414 Z= 0.281 Chirality : 0.042 0.395 1901 Planarity : 0.004 0.046 2003 Dihedral : 18.236 166.924 2492 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.89 % Allowed : 28.66 % Favored : 68.45 % 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: 0.99 (0.23), residues: 1317 helix: 2.10 (0.26), residues: 407 sheet: -0.68 (0.34), residues: 219 loop : 0.35 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 82 HIS 0.013 0.001 HIS A 215 PHE 0.019 0.001 PHE A 659 TYR 0.011 0.001 TYR A 903 ARG 0.009 0.001 ARG A1446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4412.67 seconds wall clock time: 79 minutes 49.12 seconds (4789.12 seconds total)