Starting phenix.real_space_refine on Fri Feb 16 12:21:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/02_2024/7e7q_31002_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/02_2024/7e7q_31002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/02_2024/7e7q_31002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/02_2024/7e7q_31002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/02_2024/7e7q_31002_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/02_2024/7e7q_31002_neut_updated.pdb" } resolution = 3.3 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 85 5.16 5 C 9819 2.51 5 N 2558 2.21 5 O 2809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "A PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 877": "OE1" <-> "OE2" Residue "A PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 920": "NH1" <-> "NH2" Residue "A GLU 939": "OE1" <-> "OE2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 948": "NH1" <-> "NH2" Residue "A PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 992": "NH1" <-> "NH2" Residue "A ASP 993": "OD1" <-> "OD2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A ASP 999": "OD1" <-> "OD2" Residue "A ASP 1048": "OD1" <-> "OD2" Residue "A ARG 1068": "NH1" <-> "NH2" Residue "A ASP 1079": "OD1" <-> "OD2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "A ASP 1102": "OD1" <-> "OD2" Residue "A ARG 1108": "NH1" <-> "NH2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1228": "OE1" <-> "OE2" Residue "A GLU 1271": "OE1" <-> "OE2" Residue "A PHE 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1362": "NH1" <-> "NH2" Residue "A ARG 1368": "NH1" <-> "NH2" Residue "A PHE 1373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1399": "OE1" <-> "OE2" Residue "A TYR 1414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1425": "OE1" <-> "OE2" Residue "A ARG 1443": "NH1" <-> "NH2" Residue "A TYR 1453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1517": "NH1" <-> "NH2" Residue "A GLU 1520": "OE1" <-> "OE2" Residue "A ARG 1528": "NH1" <-> "NH2" Residue "A ASP 1532": "OD1" <-> "OD2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1582": "OD1" <-> "OD2" Residue "A ARG 1585": "NH1" <-> "NH2" Residue "A ARG 1596": "NH1" <-> "NH2" Residue "A GLU 1597": "OE1" <-> "OE2" Residue "A PHE 1619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1646": "OD1" <-> "OD2" Residue "A ARG 1647": "NH1" <-> "NH2" Residue "A GLU 1670": "OE1" <-> "OE2" Residue "A PHE 1688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1705": "NH1" <-> "NH2" Residue "A TYR 1792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1814": "OE1" <-> "OE2" Residue "A ARG 1820": "NH1" <-> "NH2" Residue "A ARG 1843": "NH1" <-> "NH2" Residue "A ARG 1860": "NH1" <-> "NH2" Residue "A PHE 1861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1885": "OE1" <-> "OE2" Residue "A PHE 1900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1939": "NH1" <-> "NH2" Residue "A GLU 1942": "OE1" <-> "OE2" Residue "A ARG 1957": "NH1" <-> "NH2" Residue "A ARG 1963": "NH1" <-> "NH2" Residue "A ASP 1995": "OD1" <-> "OD2" Residue "A ASP 2024": "OD1" <-> "OD2" Residue "A ARG 2030": "NH1" <-> "NH2" Residue "A TYR 2034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2038": "NH1" <-> "NH2" Residue "A ARG 2040": "NH1" <-> "NH2" Residue "A TYR 2063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2077": "NH1" <-> "NH2" Residue "A ARG 2107": "NH1" <-> "NH2" Residue "A GLU 2119": "OE1" <-> "OE2" Residue "A ARG 2121": "NH1" <-> "NH2" Residue "A ARG 2139": "NH1" <-> "NH2" Residue "A ARG 2149": "NH1" <-> "NH2" Residue "A PHE 2161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2201": "NH1" <-> "NH2" Residue "A TYR 2203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2242": "OD1" <-> "OD2" Residue "A PHE 2245": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15279 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 14995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1958, 14995 Classifications: {'peptide': 1958} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 103, 'TRANS': 1854} Chain breaks: 15 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 641 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 527 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 13, 'GLU:plan': 21, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 381 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {' MG': 2, 'ATP': 2, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.98, per 1000 atoms: 0.52 Number of scatterers: 15279 At special positions: 0 Unit cell: (113.4, 93.96, 236.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 6 15.00 Mg 2 11.99 O 2809 8.00 N 2558 7.00 C 9819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.02 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=1.89 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=2.05 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.03 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 Links applied BETA1-3 " BMA D 3 " - " BMA D 4 " " BMA M 3 " - " BMA M 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " BETA1-6 " BMA D 3 " - " BMA D 5 " " BMA M 3 " - " BMA M 5 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 444 " " NAG A2303 " - " ASN A 504 " " NAG A2304 " - " ASN A1457 " " NAG A2305 " - " ASN A1469 " " NAG A2306 " - " ASN A1588 " " NAG A2307 " - " ASN A1662 " " NAG D 1 " - " ASN A 415 " " NAG M 1 " - " ASN A1529 " Time building additional restraints: 6.48 Conformation dependent library (CDL) restraints added in 2.8 seconds 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3662 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 12 sheets defined 45.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 3.762A pdb=" N ARG A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 34 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 37 through 44 removed outlier: 3.699A pdb=" N ASN A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 66 through 75 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 101 through 111 removed outlier: 3.809A pdb=" N TYR A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 277 through 288 Proline residue: A 282 - end of helix removed outlier: 3.658A pdb=" N GLN A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 368 through 378 Processing helix chain 'A' and resid 384 through 395 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 416 through 441 removed outlier: 4.184A pdb=" N VAL A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.523A pdb=" N ARG A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 480 No H-bonds generated for 'chain 'A' and resid 477 through 480' Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 506 through 519 removed outlier: 3.847A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 544 removed outlier: 4.131A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 608 through 622 Processing helix chain 'A' and resid 651 through 658 Proline residue: A 656 - end of helix Processing helix chain 'A' and resid 664 through 679 removed outlier: 3.508A pdb=" N VAL A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.886A pdb=" N LEU A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 721 removed outlier: 3.703A pdb=" N TRP A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 753 removed outlier: 3.961A pdb=" N THR A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 774 through 781 removed outlier: 3.694A pdb=" N CYS A 779 " --> pdb=" O HIS A 776 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 781 " --> pdb=" O LEU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 removed outlier: 4.067A pdb=" N LEU A 796 " --> pdb=" O LYS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 814 removed outlier: 3.586A pdb=" N TYR A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 removed outlier: 3.868A pdb=" N LEU A 844 " --> pdb=" O MET A 840 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 973 Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.770A pdb=" N GLN A1003 " --> pdb=" O ASP A 999 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A1004 " --> pdb=" O ALA A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1030 removed outlier: 4.028A pdb=" N GLN A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1049 removed outlier: 3.778A pdb=" N GLU A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1076 removed outlier: 3.535A pdb=" N VAL A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A1075 " --> pdb=" O SER A1071 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1121 through 1125 removed outlier: 3.791A pdb=" N LEU A1125 " --> pdb=" O ASP A1121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1121 through 1125' Processing helix chain 'A' and resid 1144 through 1151 Processing helix chain 'A' and resid 1205 through 1211 Processing helix chain 'A' and resid 1240 through 1252 removed outlier: 3.889A pdb=" N GLU A1252 " --> pdb=" O ARG A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1277 removed outlier: 3.730A pdb=" N PHE A1273 " --> pdb=" O LEU A1269 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1277 " --> pdb=" O PHE A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1368 removed outlier: 3.548A pdb=" N GLN A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1392 removed outlier: 4.601A pdb=" N LEU A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1380 - end of helix removed outlier: 3.747A pdb=" N ILE A1392 " --> pdb=" O LEU A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1409 No H-bonds generated for 'chain 'A' and resid 1407 through 1409' Processing helix chain 'A' and resid 1468 through 1476 removed outlier: 3.629A pdb=" N GLN A1475 " --> pdb=" O THR A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1545 Proline residue: A1539 - end of helix removed outlier: 3.614A pdb=" N SER A1544 " --> pdb=" O ALA A1540 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A1545 " --> pdb=" O LEU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1587 Processing helix chain 'A' and resid 1593 through 1600 removed outlier: 3.983A pdb=" N GLU A1597 " --> pdb=" O PRO A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1605 No H-bonds generated for 'chain 'A' and resid 1602 through 1605' Processing helix chain 'A' and resid 1624 through 1640 removed outlier: 4.496A pdb=" N LEU A1627 " --> pdb=" O TRP A1624 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A1628 " --> pdb=" O HIS A1625 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A1629 " --> pdb=" O ALA A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1651 No H-bonds generated for 'chain 'A' and resid 1649 through 1651' Processing helix chain 'A' and resid 1668 through 1705 removed outlier: 3.623A pdb=" N VAL A1673 " --> pdb=" O SER A1669 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A1681 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A1683 " --> pdb=" O ASP A1679 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A1692 " --> pdb=" O PHE A1688 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A1693 " --> pdb=" O SER A1689 " (cutoff:3.500A) Proline residue: A1694 - end of helix removed outlier: 4.340A pdb=" N PHE A1697 " --> pdb=" O VAL A1693 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL A1698 " --> pdb=" O PRO A1694 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A1699 " --> pdb=" O ALA A1695 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR A1700 " --> pdb=" O SER A1696 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A1701 " --> pdb=" O PHE A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1716 removed outlier: 3.688A pdb=" N SER A1716 " --> pdb=" O LEU A1712 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1749 removed outlier: 3.548A pdb=" N MET A1733 " --> pdb=" O LEU A1729 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A1737 " --> pdb=" O MET A1733 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A1738 " --> pdb=" O ASN A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1760 through 1783 removed outlier: 3.601A pdb=" N LEU A1769 " --> pdb=" O ALA A1765 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP A1772 " --> pdb=" O LEU A1768 " (cutoff:3.500A) Proline residue: A1776 - end of helix removed outlier: 4.090A pdb=" N TYR A1779 " --> pdb=" O ILE A1775 " (cutoff:3.500A) Proline residue: A1780 - end of helix removed outlier: 4.287A pdb=" N PHE A1783 " --> pdb=" O TYR A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1805 Processing helix chain 'A' and resid 1809 through 1813 Processing helix chain 'A' and resid 1821 through 1834 removed outlier: 3.584A pdb=" N PHE A1825 " --> pdb=" O THR A1821 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A1831 " --> pdb=" O ALA A1827 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE A1834 " --> pdb=" O ARG A1830 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1856 removed outlier: 4.016A pdb=" N GLY A1844 " --> pdb=" O CYS A1840 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A1846 " --> pdb=" O GLY A1842 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A1849 " --> pdb=" O LEU A1845 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A1853 " --> pdb=" O ALA A1849 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1854 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N THR A1855 " --> pdb=" O SER A1851 " (cutoff:3.500A) Processing helix chain 'A' and resid 1858 through 1860 No H-bonds generated for 'chain 'A' and resid 1858 through 1860' Processing helix chain 'A' and resid 1876 through 1900 removed outlier: 3.992A pdb=" N VAL A1883 " --> pdb=" O LEU A1879 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1884 " --> pdb=" O PHE A1880 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1887 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A1890 " --> pdb=" O GLY A1886 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1891 " --> pdb=" O VAL A1887 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A1898 " --> pdb=" O LEU A1894 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS A1899 " --> pdb=" O LEU A1895 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A1900 " --> pdb=" O VAL A1896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1986 removed outlier: 3.566A pdb=" N PHE A1982 " --> pdb=" O LYS A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2013 Processing helix chain 'A' and resid 2029 through 2038 removed outlier: 3.754A pdb=" N LEU A2033 " --> pdb=" O GLY A2029 " (cutoff:3.500A) Processing helix chain 'A' and resid 2047 through 2058 removed outlier: 3.519A pdb=" N LEU A2058 " --> pdb=" O SER A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2068 through 2070 No H-bonds generated for 'chain 'A' and resid 2068 through 2070' Processing helix chain 'A' and resid 2075 through 2083 Processing helix chain 'A' and resid 2103 through 2119 removed outlier: 3.687A pdb=" N ARG A2107 " --> pdb=" O PRO A2103 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A2108 " --> pdb=" O GLN A2104 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A2119 " --> pdb=" O SER A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2133 No H-bonds generated for 'chain 'A' and resid 2130 through 2133' Processing helix chain 'A' and resid 2154 through 2160 removed outlier: 4.061A pdb=" N LYS A2160 " --> pdb=" O HIS A2156 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2189 No H-bonds generated for 'chain 'A' and resid 2187 through 2189' Processing helix chain 'A' and resid 2216 through 2222 removed outlier: 4.895A pdb=" N LEU A2221 " --> pdb=" O ARG A2217 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU A2222 " --> pdb=" O ILE A2218 " (cutoff:3.500A) Processing helix chain 'A' and resid 2241 through 2250 Processing sheet with id= A, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.863A pdb=" N TYR A 49 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 398 through 400 Processing sheet with id= C, first strand: chain 'A' and resid 550 through 553 Processing sheet with id= D, first strand: chain 'A' and resid 631 through 636 removed outlier: 3.634A pdb=" N LYS A1616 " --> pdb=" O SER A1561 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 986 through 988 removed outlier: 5.739A pdb=" N PHE A 953 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1138 through 1142 removed outlier: 7.043A pdb=" N ILE A1132 " --> pdb=" O TYR A1139 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER A1141 " --> pdb=" O ILE A1130 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A1130 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A1113 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A1116 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A1086 " --> pdb=" O CYS A1008 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1155 through 1157 Processing sheet with id= H, first strand: chain 'A' and resid 1414 through 1417 removed outlier: 6.401A pdb=" N ILE A1521 " --> pdb=" O THR A1415 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE A1417 " --> pdb=" O ILE A1521 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A1523 " --> pdb=" O PHE A1417 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 2014 through 2017 removed outlier: 7.002A pdb=" N LEU A2091 " --> pdb=" O GLY A2015 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N CYS A2017 " --> pdb=" O LEU A2091 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU A2093 " --> pdb=" O CYS A2017 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA A2122 " --> pdb=" O VAL A2092 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A2094 " --> pdb=" O ALA A2122 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A2124 " --> pdb=" O LEU A2094 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 935 through 937 removed outlier: 3.737A pdb=" N VAL A 946 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1936 through 1939 Processing sheet with id= L, first strand: chain 'A' and resid 2140 through 2143 removed outlier: 3.519A pdb=" N ILE A2142 " --> pdb=" O CYS A2150 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS A2150 " --> pdb=" O ILE A2142 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 7.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4617 1.33 - 1.46: 3167 1.46 - 1.58: 7703 1.58 - 1.70: 10 1.70 - 1.82: 135 Bond restraints: 15632 Sorted by residual: bond pdb=" C4 ATP A2309 " pdb=" C5 ATP A2309 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" C4 ATP A2308 " pdb=" C5 ATP A2308 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.45e+01 bond pdb=" C5 ATP A2309 " pdb=" C6 ATP A2309 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.04e+01 bond pdb=" C4 ATP A2308 " pdb=" N9 ATP A2308 " ideal model delta sigma weight residual 1.374 1.316 0.058 1.00e-02 1.00e+04 3.39e+01 bond pdb=" C4 ATP A2309 " pdb=" N9 ATP A2309 " ideal model delta sigma weight residual 1.374 1.317 0.057 1.00e-02 1.00e+04 3.24e+01 ... (remaining 15627 not shown) Histogram of bond angle deviations from ideal: 97.62 - 105.43: 353 105.43 - 113.24: 8733 113.24 - 121.05: 7993 121.05 - 128.86: 4052 128.86 - 136.67: 148 Bond angle restraints: 21279 Sorted by residual: angle pdb=" PB ATP A2309 " pdb=" O3B ATP A2309 " pdb=" PG ATP A2309 " ideal model delta sigma weight residual 139.87 116.43 23.44 1.00e+00 1.00e+00 5.50e+02 angle pdb=" PB ATP A2308 " pdb=" O3B ATP A2308 " pdb=" PG ATP A2308 " ideal model delta sigma weight residual 139.87 119.55 20.32 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PA ATP A2309 " pdb=" O3A ATP A2309 " pdb=" PB ATP A2309 " ideal model delta sigma weight residual 136.83 121.41 15.42 1.00e+00 1.00e+00 2.38e+02 angle pdb=" PA ATP A2308 " pdb=" O3A ATP A2308 " pdb=" PB ATP A2308 " ideal model delta sigma weight residual 136.83 122.11 14.72 1.00e+00 1.00e+00 2.17e+02 angle pdb=" C5 ATP A2308 " pdb=" C4 ATP A2308 " pdb=" N3 ATP A2308 " ideal model delta sigma weight residual 126.80 119.03 7.77 1.00e+00 1.00e+00 6.04e+01 ... (remaining 21274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 8714 22.39 - 44.77: 617 44.77 - 67.16: 97 67.16 - 89.55: 53 89.55 - 111.93: 25 Dihedral angle restraints: 9506 sinusoidal: 3846 harmonic: 5660 Sorted by residual: dihedral pdb=" CB CYS A1444 " pdb=" SG CYS A1444 " pdb=" SG CYS A1455 " pdb=" CB CYS A1455 " ideal model delta sinusoidal sigma weight residual -86.00 -164.95 78.95 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CA GLY A 924 " pdb=" C GLY A 924 " pdb=" N TRP A 925 " pdb=" CA TRP A 925 " ideal model delta harmonic sigma weight residual -180.00 -143.63 -36.37 0 5.00e+00 4.00e-02 5.29e+01 dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A1490 " pdb=" CB CYS A1490 " ideal model delta sinusoidal sigma weight residual -86.00 -144.78 58.78 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 9503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2322 0.109 - 0.217: 153 0.217 - 0.326: 8 0.326 - 0.434: 2 0.434 - 0.543: 2 Chirality restraints: 2487 Sorted by residual: chirality pdb=" C1 NAG A2304 " pdb=" ND2 ASN A1457 " pdb=" C2 NAG A2304 " pdb=" O5 NAG A2304 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C1 NAG A2302 " pdb=" ND2 ASN A 444 " pdb=" C2 NAG A2302 " pdb=" O5 NAG A2302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CB THR A2028 " pdb=" CA THR A2028 " pdb=" OG1 THR A2028 " pdb=" CG2 THR A2028 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 2484 not shown) Planarity restraints: 2675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 380 " 0.091 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO A 381 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 961 " 0.028 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE A 961 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 961 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 961 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 961 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 961 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 961 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1735 " 0.023 2.00e-02 2.50e+03 2.16e-02 9.36e+00 pdb=" CG TYR A1735 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR A1735 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A1735 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A1735 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A1735 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A1735 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A1735 " -0.001 2.00e-02 2.50e+03 ... (remaining 2672 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 38 2.33 - 2.97: 7850 2.97 - 3.61: 20719 3.61 - 4.26: 31750 4.26 - 4.90: 55477 Nonbonded interactions: 115834 Sorted by model distance: nonbonded pdb=" O GLY A1226 " pdb=" O ALA A2135 " model vdw 1.683 3.040 nonbonded pdb=" O GLY A1154 " pdb=" O ASP A1266 " model vdw 1.738 3.040 nonbonded pdb=" O2G ATP A2309 " pdb="MG MG A2311 " model vdw 1.855 2.170 nonbonded pdb=" O3G ATP A2308 " pdb="MG MG A2310 " model vdw 1.920 2.170 nonbonded pdb=" OE1 GLN A2019 " pdb="MG MG A2311 " model vdw 1.962 2.170 ... (remaining 115829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'M' } 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: 1.570 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: 5.660 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 42.420 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.011 0.083 15632 Z= 0.697 Angle : 1.076 23.442 21279 Z= 0.624 Chirality : 0.062 0.543 2487 Planarity : 0.006 0.138 2666 Dihedral : 17.665 111.933 5826 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.16 % Favored : 88.37 % Rotamer: Outliers : 1.16 % Allowed : 1.29 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.18), residues: 1926 helix: -0.75 (0.17), residues: 911 sheet: -1.98 (0.39), residues: 155 loop : -3.24 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 31 HIS 0.011 0.002 HIS A1118 PHE 0.055 0.003 PHE A 961 TYR 0.051 0.003 TYR A1735 ARG 0.022 0.001 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1527 ASP cc_start: 0.8008 (t70) cc_final: 0.7751 (t0) REVERT: A 1566 LEU cc_start: 0.8289 (pt) cc_final: 0.8057 (pt) REVERT: A 2048 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7310 (tm-30) outliers start: 18 outliers final: 14 residues processed: 204 average time/residue: 0.2877 time to fit residues: 86.7656 Evaluate side-chains 178 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1267 THR Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1275 LYS Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1489 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 HIS A1053 HIS A1826 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15632 Z= 0.206 Angle : 0.677 9.225 21279 Z= 0.334 Chirality : 0.047 0.399 2487 Planarity : 0.005 0.101 2666 Dihedral : 13.967 99.848 2522 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.41 % Favored : 91.33 % Rotamer: Outliers : 1.48 % Allowed : 7.73 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.19), residues: 1926 helix: -0.17 (0.18), residues: 920 sheet: -1.62 (0.40), residues: 162 loop : -3.01 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 871 HIS 0.004 0.001 HIS A1941 PHE 0.025 0.001 PHE A1839 TYR 0.014 0.001 TYR A2063 ARG 0.011 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.6655 (t80) cc_final: 0.6424 (t80) REVERT: A 1233 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7142 (pp) REVERT: A 1259 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6428 (mt) REVERT: A 1271 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: A 1527 ASP cc_start: 0.7940 (t70) cc_final: 0.7690 (t0) REVERT: A 1831 LYS cc_start: 0.8010 (mttp) cc_final: 0.7585 (mtpp) REVERT: A 2086 ILE cc_start: 0.8758 (mm) cc_final: 0.8515 (mm) outliers start: 23 outliers final: 13 residues processed: 205 average time/residue: 0.2882 time to fit residues: 87.1915 Evaluate side-chains 188 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1267 THR Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1489 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 191 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 HIS A1119 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15632 Z= 0.215 Angle : 0.638 9.640 21279 Z= 0.310 Chirality : 0.046 0.374 2487 Planarity : 0.005 0.078 2666 Dihedral : 11.671 101.792 2515 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.46 % Favored : 91.28 % Rotamer: Outliers : 1.61 % Allowed : 11.86 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.19), residues: 1926 helix: 0.10 (0.18), residues: 921 sheet: -1.17 (0.40), residues: 162 loop : -2.88 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 871 HIS 0.007 0.001 HIS A 922 PHE 0.024 0.001 PHE A 961 TYR 0.014 0.001 TYR A 400 ARG 0.008 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: A 865 TYR cc_start: 0.8540 (m-80) cc_final: 0.8335 (m-10) REVERT: A 1271 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: A 1527 ASP cc_start: 0.7891 (t70) cc_final: 0.7647 (t0) REVERT: A 1735 TYR cc_start: 0.8717 (t80) cc_final: 0.8380 (t80) REVERT: A 1831 LYS cc_start: 0.7947 (mttp) cc_final: 0.7507 (mtpp) REVERT: A 2086 ILE cc_start: 0.8773 (mm) cc_final: 0.8543 (mm) REVERT: A 2200 GLU cc_start: 0.7121 (pt0) cc_final: 0.6796 (pp20) outliers start: 25 outliers final: 13 residues processed: 202 average time/residue: 0.2728 time to fit residues: 82.1593 Evaluate side-chains 187 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1267 THR Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1681 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15632 Z= 0.172 Angle : 0.598 9.654 21279 Z= 0.290 Chirality : 0.045 0.353 2487 Planarity : 0.004 0.068 2666 Dihedral : 10.165 103.507 2505 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.32 % Favored : 92.47 % Rotamer: Outliers : 2.00 % Allowed : 13.47 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.19), residues: 1926 helix: 0.23 (0.18), residues: 928 sheet: -0.92 (0.41), residues: 162 loop : -2.75 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 871 HIS 0.003 0.001 HIS A1118 PHE 0.018 0.001 PHE A 961 TYR 0.013 0.001 TYR A 400 ARG 0.006 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 1.787 Fit side-chains REVERT: A 49 TYR cc_start: 0.6623 (t80) cc_final: 0.6391 (t80) REVERT: A 922 HIS cc_start: 0.5145 (t70) cc_final: 0.4781 (t-170) REVERT: A 1047 GLU cc_start: 0.8067 (tp30) cc_final: 0.7728 (tp30) REVERT: A 1085 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8758 (pp) REVERT: A 1271 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: A 1274 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 1527 ASP cc_start: 0.7866 (t70) cc_final: 0.7621 (t0) REVERT: A 1735 TYR cc_start: 0.8657 (t80) cc_final: 0.8286 (t80) REVERT: A 1814 GLU cc_start: 0.7738 (pp20) cc_final: 0.7485 (pp20) REVERT: A 1831 LYS cc_start: 0.7918 (mttp) cc_final: 0.7471 (mtpp) REVERT: A 2063 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7245 (p90) REVERT: A 2086 ILE cc_start: 0.8754 (mm) cc_final: 0.8545 (mm) REVERT: A 2200 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: A 2205 MET cc_start: 0.5901 (mmp) cc_final: 0.5415 (mmm) outliers start: 31 outliers final: 15 residues processed: 211 average time/residue: 0.2805 time to fit residues: 87.8972 Evaluate side-chains 195 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain A residue 2200 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.0170 chunk 160 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 169 optimal weight: 0.0050 chunk 47 optimal weight: 4.9990 overall best weight: 1.0034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15632 Z= 0.186 Angle : 0.587 9.709 21279 Z= 0.286 Chirality : 0.045 0.338 2487 Planarity : 0.004 0.057 2666 Dihedral : 9.495 104.700 2503 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.20 % Favored : 91.64 % Rotamer: Outliers : 2.45 % Allowed : 14.18 % Favored : 83.38 % 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: -1.49 (0.19), residues: 1926 helix: 0.32 (0.18), residues: 934 sheet: -0.58 (0.44), residues: 151 loop : -2.67 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 871 HIS 0.004 0.001 HIS A1118 PHE 0.018 0.001 PHE A 961 TYR 0.013 0.001 TYR A 400 ARG 0.002 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 183 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.6612 (t80) cc_final: 0.6391 (t80) REVERT: A 1085 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8750 (pp) REVERT: A 1271 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: A 1274 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 1527 ASP cc_start: 0.7818 (t70) cc_final: 0.7577 (t0) REVERT: A 1735 TYR cc_start: 0.8670 (t80) cc_final: 0.8301 (t80) REVERT: A 1814 GLU cc_start: 0.7724 (pp20) cc_final: 0.7466 (pp20) REVERT: A 1831 LYS cc_start: 0.7914 (mttp) cc_final: 0.7453 (mtpp) REVERT: A 2063 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7238 (p90) REVERT: A 2086 ILE cc_start: 0.8775 (mm) cc_final: 0.8545 (mm) REVERT: A 2205 MET cc_start: 0.6083 (mmp) cc_final: 0.5849 (mmp) outliers start: 38 outliers final: 20 residues processed: 211 average time/residue: 0.2751 time to fit residues: 87.1906 Evaluate side-chains 203 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2063 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 62 optimal weight: 0.0770 chunk 99 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 HIS ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15632 Z= 0.156 Angle : 0.565 9.690 21279 Z= 0.275 Chirality : 0.043 0.325 2487 Planarity : 0.004 0.054 2666 Dihedral : 9.040 105.106 2503 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.68 % Favored : 92.26 % Rotamer: Outliers : 2.19 % Allowed : 15.34 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.20), residues: 1926 helix: 0.41 (0.18), residues: 938 sheet: -0.61 (0.43), residues: 161 loop : -2.64 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 871 HIS 0.003 0.000 HIS A1118 PHE 0.015 0.001 PHE A 961 TYR 0.013 0.001 TYR A 400 ARG 0.003 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: A 113 LEU cc_start: 0.7439 (mm) cc_final: 0.7216 (mp) REVERT: A 922 HIS cc_start: 0.5099 (t70) cc_final: 0.4748 (t-170) REVERT: A 1271 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: A 1274 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8262 (mm) REVERT: A 1527 ASP cc_start: 0.7825 (t70) cc_final: 0.7588 (t0) REVERT: A 1735 TYR cc_start: 0.8618 (t80) cc_final: 0.8250 (t80) REVERT: A 1814 GLU cc_start: 0.7708 (pp20) cc_final: 0.7447 (pp20) REVERT: A 1831 LYS cc_start: 0.7911 (mttp) cc_final: 0.7443 (mtpp) REVERT: A 2063 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7098 (p90) REVERT: A 2086 ILE cc_start: 0.8739 (mm) cc_final: 0.8536 (mm) REVERT: A 2145 LYS cc_start: 0.7850 (pttt) cc_final: 0.7633 (ptpp) REVERT: A 2205 MET cc_start: 0.6143 (mmp) cc_final: 0.5688 (mmm) outliers start: 34 outliers final: 17 residues processed: 204 average time/residue: 0.2725 time to fit residues: 83.9034 Evaluate side-chains 197 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1614 ASN Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2063 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.0170 chunk 21 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 ASN A1053 HIS ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15632 Z= 0.193 Angle : 0.581 9.729 21279 Z= 0.283 Chirality : 0.044 0.317 2487 Planarity : 0.004 0.051 2666 Dihedral : 8.864 104.251 2499 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.20 % Favored : 91.74 % Rotamer: Outliers : 1.87 % Allowed : 16.30 % Favored : 81.83 % 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: -1.33 (0.20), residues: 1926 helix: 0.44 (0.18), residues: 935 sheet: -0.55 (0.43), residues: 161 loop : -2.58 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 871 HIS 0.003 0.001 HIS A1406 PHE 0.016 0.001 PHE A 836 TYR 0.013 0.001 TYR A 400 ARG 0.001 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8605 (pt0) REVERT: A 113 LEU cc_start: 0.7469 (mm) cc_final: 0.7244 (mp) REVERT: A 951 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8708 (tp) REVERT: A 1271 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: A 1274 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8254 (mm) REVERT: A 1527 ASP cc_start: 0.7851 (t70) cc_final: 0.7609 (t0) REVERT: A 1735 TYR cc_start: 0.8670 (t80) cc_final: 0.8302 (t80) REVERT: A 1814 GLU cc_start: 0.7725 (pp20) cc_final: 0.7442 (pp20) REVERT: A 1831 LYS cc_start: 0.7908 (mttp) cc_final: 0.7434 (mtpp) REVERT: A 2063 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7046 (p90) REVERT: A 2086 ILE cc_start: 0.8777 (mm) cc_final: 0.8540 (mm) REVERT: A 2145 LYS cc_start: 0.7865 (pttt) cc_final: 0.7619 (ptpp) outliers start: 29 outliers final: 21 residues processed: 200 average time/residue: 0.2773 time to fit residues: 83.0491 Evaluate side-chains 201 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1614 ASN Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1769 LEU Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2063 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 50.0000 chunk 147 optimal weight: 0.0980 chunk 170 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15632 Z= 0.153 Angle : 0.554 9.664 21279 Z= 0.269 Chirality : 0.043 0.315 2487 Planarity : 0.004 0.063 2666 Dihedral : 8.565 101.751 2498 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.22 % Favored : 92.73 % Rotamer: Outliers : 2.00 % Allowed : 16.24 % Favored : 81.77 % 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: -1.19 (0.20), residues: 1926 helix: 0.55 (0.18), residues: 929 sheet: -0.48 (0.44), residues: 161 loop : -2.49 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 871 HIS 0.002 0.000 HIS A1118 PHE 0.015 0.001 PHE A 961 TYR 0.021 0.001 TYR A 49 ARG 0.001 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8547 (pt0) REVERT: A 922 HIS cc_start: 0.5008 (t70) cc_final: 0.4662 (t-170) REVERT: A 1271 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: A 1274 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8211 (mm) REVERT: A 1527 ASP cc_start: 0.7822 (t70) cc_final: 0.7596 (t0) REVERT: A 1735 TYR cc_start: 0.8616 (t80) cc_final: 0.8288 (t80) REVERT: A 1814 GLU cc_start: 0.7639 (pp20) cc_final: 0.7343 (pp20) REVERT: A 1831 LYS cc_start: 0.7894 (mttp) cc_final: 0.7434 (mtpp) REVERT: A 2063 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6894 (p90) REVERT: A 2086 ILE cc_start: 0.8741 (mm) cc_final: 0.8525 (mm) REVERT: A 2145 LYS cc_start: 0.7804 (pttt) cc_final: 0.7550 (ptpp) outliers start: 31 outliers final: 22 residues processed: 211 average time/residue: 0.2770 time to fit residues: 88.1977 Evaluate side-chains 207 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1614 ASN Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2063 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2075 ASN A2096 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15632 Z= 0.214 Angle : 0.592 9.749 21279 Z= 0.287 Chirality : 0.045 0.314 2487 Planarity : 0.004 0.064 2666 Dihedral : 8.623 99.589 2498 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.05 % Favored : 91.85 % Rotamer: Outliers : 1.87 % Allowed : 16.75 % Favored : 81.38 % 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: -1.20 (0.20), residues: 1926 helix: 0.54 (0.18), residues: 936 sheet: -0.53 (0.44), residues: 161 loop : -2.50 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 871 HIS 0.004 0.001 HIS A1406 PHE 0.018 0.001 PHE A 961 TYR 0.020 0.001 TYR A 49 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8648 (pt0) REVERT: A 1271 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: A 1527 ASP cc_start: 0.7826 (t70) cc_final: 0.7586 (t0) REVERT: A 1735 TYR cc_start: 0.8710 (t80) cc_final: 0.8413 (t80) REVERT: A 1814 GLU cc_start: 0.7647 (pp20) cc_final: 0.7326 (pp20) REVERT: A 1831 LYS cc_start: 0.7862 (mttp) cc_final: 0.7429 (mtpp) REVERT: A 2063 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.6843 (p90) REVERT: A 2086 ILE cc_start: 0.8792 (mm) cc_final: 0.8542 (mm) REVERT: A 2096 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8070 (mm110) REVERT: A 2145 LYS cc_start: 0.7915 (pttt) cc_final: 0.7651 (ptpp) outliers start: 29 outliers final: 21 residues processed: 204 average time/residue: 0.2718 time to fit residues: 83.7848 Evaluate side-chains 200 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1614 ASN Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain A residue 2096 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 0.0270 chunk 128 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 0.0970 chunk 16 optimal weight: 40.0000 chunk 119 optimal weight: 0.0770 chunk 94 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2096 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15632 Z= 0.166 Angle : 0.577 10.399 21279 Z= 0.278 Chirality : 0.044 0.309 2487 Planarity : 0.004 0.064 2666 Dihedral : 8.453 97.783 2496 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.68 % Favored : 92.21 % Rotamer: Outliers : 1.68 % Allowed : 16.82 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1926 helix: 0.57 (0.18), residues: 932 sheet: -0.46 (0.44), residues: 161 loop : -2.46 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 871 HIS 0.002 0.001 HIS A1406 PHE 0.019 0.001 PHE A1839 TYR 0.018 0.001 TYR A 49 ARG 0.001 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8600 (pt0) REVERT: A 922 HIS cc_start: 0.5011 (t70) cc_final: 0.4662 (t-170) REVERT: A 1271 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: A 1527 ASP cc_start: 0.7817 (t70) cc_final: 0.7583 (t0) REVERT: A 1735 TYR cc_start: 0.8680 (t80) cc_final: 0.8382 (t80) REVERT: A 1814 GLU cc_start: 0.7635 (pp20) cc_final: 0.7319 (pp20) REVERT: A 1831 LYS cc_start: 0.7855 (mttp) cc_final: 0.7422 (mtpp) REVERT: A 2063 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.6749 (p90) REVERT: A 2086 ILE cc_start: 0.8774 (mm) cc_final: 0.8530 (mm) REVERT: A 2096 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8392 (mt0) REVERT: A 2145 LYS cc_start: 0.7859 (pttt) cc_final: 0.7597 (ptpp) outliers start: 26 outliers final: 19 residues processed: 198 average time/residue: 0.2722 time to fit residues: 80.7639 Evaluate side-chains 199 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1457 ASN Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1614 ASN Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain A residue 2096 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 159 optimal weight: 0.1980 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2096 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108901 restraints weight = 21489.600| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.49 r_work: 0.2984 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15632 Z= 0.159 Angle : 0.570 10.951 21279 Z= 0.274 Chirality : 0.044 0.305 2487 Planarity : 0.004 0.064 2666 Dihedral : 8.321 95.469 2496 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.63 % Favored : 92.32 % Rotamer: Outliers : 1.87 % Allowed : 16.88 % Favored : 81.25 % 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: -1.10 (0.20), residues: 1926 helix: 0.62 (0.18), residues: 932 sheet: -0.46 (0.45), residues: 161 loop : -2.43 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 871 HIS 0.002 0.001 HIS A1406 PHE 0.016 0.001 PHE A 961 TYR 0.017 0.001 TYR A 49 ARG 0.001 0.000 ARG A1939 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3227.32 seconds wall clock time: 59 minutes 15.23 seconds (3555.23 seconds total)