Starting phenix.real_space_refine on Tue Apr 9 07:26:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7i_31000/04_2024/7e7i_31000_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7i_31000/04_2024/7e7i_31000.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/7e7i_31000/04_2024/7e7i_31000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7i_31000/04_2024/7e7i_31000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7i_31000/04_2024/7e7i_31000_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7i_31000/04_2024/7e7i_31000_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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 85 5.16 5 C 10136 2.51 5 N 2618 2.21 5 O 2883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 784": "OD1" <-> "OD2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "A PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 858": "OD1" <-> "OD2" Residue "A PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 921": "OE1" <-> "OE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A ARG 1068": "NH1" <-> "NH2" Residue "A ASP 1079": "OD1" <-> "OD2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1108": "NH1" <-> "NH2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1161": "NH1" <-> "NH2" Residue "A ASP 1202": "OD1" <-> "OD2" Residue "A ASP 1204": "OD1" <-> "OD2" Residue "A GLU 1228": "OE1" <-> "OE2" Residue "A PHE 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1266": "OD1" <-> "OD2" Residue "A PHE 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1362": "NH1" <-> "NH2" Residue "A PHE 1363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1368": "NH1" <-> "NH2" Residue "A GLU 1399": "OE1" <-> "OE2" Residue "A TYR 1414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1443": "NH1" <-> "NH2" Residue "A GLU 1504": "OE1" <-> "OE2" Residue "A ARG 1517": "NH1" <-> "NH2" Residue "A ARG 1528": "NH1" <-> "NH2" Residue "A PHE 1550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1585": "NH1" <-> "NH2" Residue "A ARG 1596": "NH1" <-> "NH2" Residue "A PHE 1619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1647": "NH1" <-> "NH2" Residue "A TYR 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1705": "NH1" <-> "NH2" Residue "A PHE 1801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1860": "NH1" <-> "NH2" Residue "A PHE 1861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1863": "OE1" <-> "OE2" Residue "A GLU 1864": "OE1" <-> "OE2" Residue "A ARG 1898": "NH1" <-> "NH2" Residue "A ARG 1925": "NH1" <-> "NH2" Residue "A ARG 1939": "NH1" <-> "NH2" Residue "A ARG 1957": "NH1" <-> "NH2" Residue "A GLU 1966": "OE1" <-> "OE2" Residue "A ASP 1988": "OD1" <-> "OD2" Residue "A ASP 2024": "OD1" <-> "OD2" Residue "A GLU 2025": "OE1" <-> "OE2" Residue "A ARG 2030": "NH1" <-> "NH2" Residue "A ARG 2038": "NH1" <-> "NH2" Residue "A ARG 2040": "NH1" <-> "NH2" Residue "A GLU 2048": "OE1" <-> "OE2" Residue "A ARG 2077": "NH1" <-> "NH2" Residue "A ASP 2095": "OD1" <-> "OD2" Residue "A ASP 2102": "OD1" <-> "OD2" Residue "A ARG 2107": "NH1" <-> "NH2" Residue "A ARG 2118": "NH1" <-> "NH2" Residue "A ARG 2121": "NH1" <-> "NH2" Residue "A ARG 2139": "NH1" <-> "NH2" Residue "A ARG 2149": "NH1" <-> "NH2" Residue "A TYR 2165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2242": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15724 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2011, 15402 Classifications: {'peptide': 2011} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 98, 'TRANS': 1912} Chain breaks: 12 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 15, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 19, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 391 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: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 200 Unusual residues: {'3PE': 2, 'NAG': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 8.39, per 1000 atoms: 0.53 Number of scatterers: 15724 At special positions: 0 Unit cell: (100.44, 104.76, 241.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 2 15.00 O 2883 8.00 N 2618 7.00 C 10136 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=2.04 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=1.92 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=2.15 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=1, 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 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 3.0 seconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 8 sheets defined 44.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.89 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.957A pdb=" N LYS A 19 " --> pdb=" O TRP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 36 removed outlier: 3.560A pdb=" N LEU A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.657A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (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 67 through 75 Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.960A pdb=" N TYR A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 135 removed outlier: 3.540A pdb=" N SER A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 234 through 237 No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.543A pdb=" N ILE A 284 " --> pdb=" O MET A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 373 through 376 No H-bonds generated for 'chain 'A' and resid 373 through 376' Processing helix chain 'A' and resid 386 through 394 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 405 through 443 removed outlier: 4.083A pdb=" N ASN A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N SER A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TRP A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 4.246A 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 463 through 470 removed outlier: 3.685A pdb=" N GLU A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 504 through 516 removed outlier: 3.904A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 544 removed outlier: 4.046A 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 621 Processing helix chain 'A' and resid 647 through 679 removed outlier: 3.844A pdb=" N ASN A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Proline residue: A 656 - end of helix removed outlier: 3.940A pdb=" N TRP A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 664 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 670 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A 673 " --> pdb=" O MET A 669 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.736A pdb=" N LEU A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 721 removed outlier: 3.607A pdb=" N SER A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 714 " --> pdb=" O MET A 710 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 754 removed outlier: 3.864A pdb=" N PHE A 734 " --> pdb=" O PRO A 730 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 779 removed outlier: 3.522A pdb=" N ALA A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR A 773 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 774 " --> pdb=" O PHE A 770 " (cutoff:3.500A) Proline residue: A 775 - end of helix removed outlier: 3.834A pdb=" N LEU A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 removed outlier: 3.587A pdb=" N SER A 795 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 796 " --> pdb=" O LYS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 814 removed outlier: 3.681A pdb=" N GLY A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 859 removed outlier: 3.829A pdb=" N LEU A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR A 856 " --> pdb=" O LEU A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 977 Processing helix chain 'A' and resid 1000 through 1003 Processing helix chain 'A' and resid 1020 through 1032 removed outlier: 3.716A pdb=" N LYS A1031 " --> pdb=" O TYR A1027 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1048 removed outlier: 3.512A pdb=" N GLU A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1076 removed outlier: 4.240A pdb=" N ALA A1075 " --> pdb=" O SER A1071 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 3.977A pdb=" N ARG A1098 " --> pdb=" O PRO A1094 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A1099 " --> pdb=" O TYR A1095 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A1103 " --> pdb=" O SER A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1125 No H-bonds generated for 'chain 'A' and resid 1122 through 1125' Processing helix chain 'A' and resid 1144 through 1151 removed outlier: 3.556A pdb=" N PHE A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 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 1254 through 1257 No H-bonds generated for 'chain 'A' and resid 1254 through 1257' Processing helix chain 'A' and resid 1269 through 1277 removed outlier: 3.784A pdb=" N LYS A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1368 removed outlier: 3.852A pdb=" N GLN A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1360 " --> pdb=" O GLN A1356 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1375 removed outlier: 3.919A pdb=" N ALA A1375 " --> pdb=" O LYS A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1391 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 1427 through 1430 No H-bonds generated for 'chain 'A' and resid 1427 through 1430' Processing helix chain 'A' and resid 1468 through 1476 removed outlier: 3.758A pdb=" N GLN A1475 " --> pdb=" O THR A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1536 removed outlier: 4.493A pdb=" N VAL A1535 " --> pdb=" O SER A1531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A1536 " --> pdb=" O ASP A1532 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1545 removed outlier: 4.391A pdb=" N SER A1544 " --> pdb=" O ALA A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1587 removed outlier: 3.843A pdb=" N PHE A1579 " --> pdb=" O ALA A1575 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A1587 " --> pdb=" O LEU A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1598 No H-bonds generated for 'chain 'A' and resid 1595 through 1598' 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 1627 through 1640 removed outlier: 3.828A pdb=" N ASN A1632 " --> pdb=" O VAL A1628 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A1633 " --> pdb=" O SER A1629 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1639 " --> pdb=" O HIS A1635 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A1640 " --> pdb=" O ASN A1636 " (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 1690 removed outlier: 4.573A pdb=" N VAL A1673 " --> pdb=" O SER A1669 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL A1678 " --> pdb=" O LEU A1674 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A1679 " --> pdb=" O THR A1675 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A1681 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A1684 " --> pdb=" O ALA A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1717 removed outlier: 3.776A pdb=" N VAL A1698 " --> pdb=" O PRO A1694 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A1699 " --> pdb=" O ALA A1695 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR A1700 " --> pdb=" O SER A1696 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A1701 " --> pdb=" O PHE A1697 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A1708 " --> pdb=" O GLU A1704 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A1709 " --> pdb=" O ARG A1705 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LYS A1710 " --> pdb=" O VAL A1706 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N HIS A1711 " --> pdb=" O ASN A1707 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1716 " --> pdb=" O LEU A1712 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1749 removed outlier: 3.571A pdb=" N MET A1733 " --> pdb=" O LEU A1729 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A1737 " --> pdb=" O MET A1733 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A1738 " --> pdb=" O ASN A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1760 through 1783 removed outlier: 3.509A pdb=" N TYR A1770 " --> pdb=" O LEU A1766 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A1771 " --> pdb=" O LEU A1767 " (cutoff:3.500A) Proline residue: A1776 - end of helix removed outlier: 3.635A pdb=" N TYR A1779 " --> pdb=" O ILE A1775 " (cutoff:3.500A) Proline residue: A1780 - end of helix removed outlier: 4.258A pdb=" N PHE A1783 " --> pdb=" O TYR A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1814 removed outlier: 4.140A pdb=" N CYS A1797 " --> pdb=" O VAL A1793 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A1798 " --> pdb=" O ALA A1794 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A1800 " --> pdb=" O SER A1796 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A1803 " --> pdb=" O ASN A1799 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A1805 " --> pdb=" O PHE A1801 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A1806 " --> pdb=" O ILE A1802 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A1807 " --> pdb=" O GLY A1803 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE A1809 " --> pdb=" O ASN A1805 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR A1810 " --> pdb=" O SER A1806 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE A1811 " --> pdb=" O SER A1807 " (cutoff:3.500A) Processing helix chain 'A' and resid 1822 through 1832 removed outlier: 3.593A pdb=" N VAL A1828 " --> pdb=" O ARG A1824 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A1831 " --> pdb=" O ALA A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1845 removed outlier: 3.936A pdb=" N GLY A1844 " --> pdb=" O CYS A1840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1860 removed outlier: 3.993A pdb=" N GLN A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A1858 " --> pdb=" O VAL A1854 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A1859 " --> pdb=" O THR A1855 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A1860 " --> pdb=" O ASP A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1876 through 1893 removed outlier: 3.686A pdb=" N VAL A1883 " --> pdb=" O LEU A1879 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A1887 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A1889 " --> pdb=" O GLU A1885 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE A1890 " --> pdb=" O GLY A1886 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1926 Processing helix chain 'A' and resid 1979 through 1985 Processing helix chain 'A' and resid 2007 through 2010 No H-bonds generated for 'chain 'A' and resid 2007 through 2010' Processing helix chain 'A' and resid 2029 through 2038 removed outlier: 3.652A pdb=" N LEU A2033 " --> pdb=" O GLY A2029 " (cutoff:3.500A) Processing helix chain 'A' and resid 2047 through 2058 removed outlier: 3.565A pdb=" N LYS A2056 " --> pdb=" O ASN A2052 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A2058 " --> pdb=" O SER A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2085 removed outlier: 3.783A pdb=" N LEU A2085 " --> pdb=" O THR A2081 " (cutoff:3.500A) Processing helix chain 'A' and resid 2103 through 2119 removed outlier: 4.241A pdb=" N ARG A2107 " --> pdb=" O PRO A2103 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A2108 " --> pdb=" O GLN A2104 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A2109 " --> pdb=" O ALA A2105 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A2112 " --> pdb=" O MET A2108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A2117 " --> pdb=" O ILE A2113 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU A2119 " --> pdb=" O SER A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2135 No H-bonds generated for 'chain 'A' and resid 2132 through 2135' Processing helix chain 'A' and resid 2154 through 2160 removed outlier: 3.571A pdb=" N SER A2159 " --> pdb=" O GLN A2155 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A2160 " --> pdb=" O HIS A2156 " (cutoff:3.500A) Processing helix chain 'A' and resid 2183 through 2192 removed outlier: 3.609A pdb=" N GLN A2187 " --> pdb=" O ASN A2183 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN A2190 " --> pdb=" O GLU A2186 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLY A2191 " --> pdb=" O GLN A2187 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN A2192 " --> pdb=" O PHE A2188 " (cutoff:3.500A) Processing helix chain 'A' and resid 2241 through 2251 removed outlier: 3.649A pdb=" N VAL A2246 " --> pdb=" O GLN A2243 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A2250 " --> pdb=" O ASN A2247 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN A2251 " --> pdb=" O PHE A2248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.575A pdb=" N PHE A 642 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 567 through 571 Processing sheet with id= C, first strand: chain 'A' and resid 632 through 636 removed outlier: 6.638A pdb=" N ILE A1615 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLN A 635 " --> pdb=" O ILE A1615 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL A1617 " --> pdb=" O GLN A 635 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A1616 " --> pdb=" O SER A1561 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N TYR A1414 " --> pdb=" O TYR A1557 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY A1559 " --> pdb=" O TYR A1414 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE A1416 " --> pdb=" O GLY A1559 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER A1561 " --> pdb=" O PHE A1416 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE A1521 " --> pdb=" O THR A1415 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE A1417 " --> pdb=" O ILE A1521 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN A1523 " --> pdb=" O PHE A1417 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 930 through 932 removed outlier: 3.664A pdb=" N THR A 986 " --> pdb=" O LYS A 932 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1138 through 1142 removed outlier: 6.974A pdb=" N ILE A1132 " --> pdb=" O TYR A1139 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A1141 " --> pdb=" O ILE A1130 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A1130 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A1113 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A1084 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A1086 " --> pdb=" O CYS A1008 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 2091 through 2093 removed outlier: 6.931A pdb=" N ALA A2122 " --> pdb=" O VAL A2092 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 2166 through 2169 Processing sheet with id= H, first strand: chain 'A' and resid 1159 through 1161 removed outlier: 3.655A pdb=" N VAL A1160 " --> pdb=" O SER A1261 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER A1261 " --> pdb=" O VAL A1160 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 459 hydrogen bonds defined for protein. 1350 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: 5.39 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3303 1.33 - 1.45: 3881 1.45 - 1.58: 8753 1.58 - 1.70: 4 1.70 - 1.83: 137 Bond restraints: 16078 Sorted by residual: bond pdb=" C21 3PE A2309 " pdb=" O21 3PE A2309 " ideal model delta sigma weight residual 1.316 1.451 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C21 3PE A2308 " pdb=" O21 3PE A2308 " ideal model delta sigma weight residual 1.316 1.449 -0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C31 3PE A2308 " pdb=" O31 3PE A2308 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C31 3PE A2309 " pdb=" O31 3PE A2309 " ideal model delta sigma weight residual 1.331 1.444 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C1 NAG A2304 " pdb=" O5 NAG A2304 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 16073 not shown) Histogram of bond angle deviations from ideal: 74.09 - 87.37: 1 87.37 - 100.65: 29 100.65 - 113.94: 9664 113.94 - 127.22: 11933 127.22 - 140.50: 209 Bond angle restraints: 21836 Sorted by residual: angle pdb=" N ASN A1235 " pdb=" CA ASN A1235 " pdb=" C ASN A1235 " ideal model delta sigma weight residual 109.14 74.09 35.05 1.49e+00 4.50e-01 5.53e+02 angle pdb=" N LYS A1236 " pdb=" CA LYS A1236 " pdb=" CB LYS A1236 " ideal model delta sigma weight residual 110.49 140.50 -30.01 1.69e+00 3.50e-01 3.15e+02 angle pdb=" N LYS A1236 " pdb=" CA LYS A1236 " pdb=" C LYS A1236 " ideal model delta sigma weight residual 110.80 89.03 21.77 2.13e+00 2.20e-01 1.04e+02 angle pdb=" N CYS A1444 " pdb=" CA CYS A1444 " pdb=" C CYS A1444 " ideal model delta sigma weight residual 112.93 119.97 -7.04 1.12e+00 7.97e-01 3.95e+01 angle pdb=" N GLU A1666 " pdb=" CA GLU A1666 " pdb=" C GLU A1666 " ideal model delta sigma weight residual 114.04 107.03 7.01 1.24e+00 6.50e-01 3.20e+01 ... (remaining 21831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 9087 25.04 - 50.09: 540 50.09 - 75.13: 90 75.13 - 100.17: 51 100.17 - 125.22: 18 Dihedral angle restraints: 9786 sinusoidal: 3970 harmonic: 5816 Sorted by residual: dihedral pdb=" N LYS A1236 " pdb=" C LYS A1236 " pdb=" CA LYS A1236 " pdb=" CB LYS A1236 " ideal model delta harmonic sigma weight residual 122.80 144.55 -21.75 0 2.50e+00 1.60e-01 7.57e+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 -156.07 70.07 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" N ASN A1235 " pdb=" C ASN A1235 " pdb=" CA ASN A1235 " pdb=" CB ASN A1235 " ideal model delta harmonic sigma weight residual 122.80 104.80 18.00 0 2.50e+00 1.60e-01 5.18e+01 ... (remaining 9783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2448 0.131 - 0.263: 78 0.263 - 0.394: 11 0.394 - 0.526: 1 0.526 - 0.657: 1 Chirality restraints: 2539 Sorted by residual: chirality pdb=" CA LYS A1236 " pdb=" N LYS A1236 " pdb=" C LYS A1236 " pdb=" CB LYS A1236 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" C1 NAG A2306 " pdb=" ND2 ASN A1588 " pdb=" C2 NAG A2306 " pdb=" O5 NAG A2306 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.86e+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 2.17 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 2536 not shown) Planarity restraints: 2753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.063 2.00e-02 2.50e+03 5.72e-02 4.09e+01 pdb=" CG ASN A 98 " -0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " -0.058 2.00e-02 2.50e+03 pdb=" C1 NAG A2301 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" CG ASN A 98 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1746 " -0.024 2.00e-02 2.50e+03 2.13e-02 7.95e+00 pdb=" CG PHE A1746 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A1746 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A1746 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A1746 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1746 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A1746 " -0.005 2.00e-02 2.50e+03 ... (remaining 2750 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 25 2.25 - 2.92: 7003 2.92 - 3.58: 20902 3.58 - 4.24: 33531 4.24 - 4.90: 57401 Nonbonded interactions: 118862 Sorted by model distance: nonbonded pdb=" SD MET A1163 " pdb=" N LEU A1201 " model vdw 1.593 2.880 nonbonded pdb=" CE MET A1163 " pdb=" O GLN A1199 " model vdw 1.614 3.460 nonbonded pdb=" SD MET A1163 " pdb=" CA LEU A1201 " model vdw 1.623 3.830 nonbonded pdb=" CE MET A1163 " pdb=" C VAL A1200 " model vdw 1.697 3.690 nonbonded pdb=" O LEU A1254 " pdb=" CD1 LEU A1257 " model vdw 1.722 3.460 ... (remaining 118857 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.780 Check model and map are aligned: 0.220 Set scattering table: 0.160 Process input model: 44.510 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 0.135 16078 Z= 0.718 Angle : 1.164 35.046 21836 Z= 0.617 Chirality : 0.064 0.657 2539 Planarity : 0.006 0.064 2744 Dihedral : 18.445 125.216 6008 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.26 % Favored : 83.98 % Rotamer: Outliers : 1.82 % Allowed : 1.13 % Favored : 97.04 % Cbeta Deviations : 0.05 % 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: -4.06 (0.17), residues: 1985 helix: -1.84 (0.16), residues: 942 sheet: -2.59 (0.37), residues: 168 loop : -3.71 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 697 HIS 0.013 0.002 HIS A 423 PHE 0.049 0.003 PHE A1746 TYR 0.040 0.003 TYR A 400 ARG 0.020 0.001 ARG A1939 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.645 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8738 (mmp) cc_final: 0.8344 (mmp) REVERT: A 1202 ASP cc_start: 0.5381 (OUTLIER) cc_final: 0.5007 (m-30) REVERT: A 1223 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: A 1241 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6887 (mtm-85) REVERT: A 1704 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 1939 ARG cc_start: 0.7582 (tmt170) cc_final: 0.6834 (tmt170) REVERT: A 2025 GLU cc_start: 0.8361 (pt0) cc_final: 0.7959 (pm20) outliers start: 29 outliers final: 20 residues processed: 208 average time/residue: 0.2958 time to fit residues: 92.4978 Evaluate side-chains 183 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1257 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 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1273 PHE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1491 SER Chi-restraints excluded: chain A residue 1492 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 182 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16078 Z= 0.196 Angle : 0.754 9.448 21836 Z= 0.370 Chirality : 0.047 0.410 2539 Planarity : 0.005 0.059 2744 Dihedral : 14.911 116.478 2627 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.88 % Favored : 88.72 % Rotamer: Outliers : 1.76 % Allowed : 8.74 % Favored : 89.50 % 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: -3.31 (0.18), residues: 1985 helix: -1.13 (0.17), residues: 927 sheet: -1.77 (0.39), residues: 170 loop : -3.52 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 605 HIS 0.006 0.001 HIS A1941 PHE 0.023 0.001 PHE A2193 TYR 0.020 0.001 TYR A 340 ARG 0.004 0.000 ARG A1161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: A 1202 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.5491 (m-30) REVERT: A 1223 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: A 1241 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7257 (mtm-85) REVERT: A 1276 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.7977 (t) REVERT: A 2025 GLU cc_start: 0.8308 (pt0) cc_final: 0.7980 (pm20) outliers start: 28 outliers final: 18 residues processed: 207 average time/residue: 0.2947 time to fit residues: 91.4533 Evaluate side-chains 180 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2067 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 162 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1871 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16078 Z= 0.337 Angle : 0.773 10.175 21836 Z= 0.377 Chirality : 0.050 0.410 2539 Planarity : 0.005 0.058 2744 Dihedral : 13.391 116.529 2613 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.90 % Favored : 86.80 % Rotamer: Outliers : 2.52 % Allowed : 12.83 % Favored : 84.65 % 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: -3.06 (0.18), residues: 1985 helix: -0.96 (0.17), residues: 932 sheet: -1.68 (0.38), residues: 187 loop : -3.36 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 605 HIS 0.008 0.001 HIS A1941 PHE 0.020 0.002 PHE A1416 TYR 0.031 0.002 TYR A 400 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7959 (tp40) REVERT: A 689 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8096 (mm-40) REVERT: A 727 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.7344 (p90) REVERT: A 992 ARG cc_start: 0.7613 (ptt180) cc_final: 0.7359 (ptt90) REVERT: A 1155 LEU cc_start: 0.8365 (mp) cc_final: 0.8149 (mp) REVERT: A 1202 ASP cc_start: 0.5753 (OUTLIER) cc_final: 0.5547 (m-30) REVERT: A 1223 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: A 1241 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7317 (mtm-85) REVERT: A 1493 ARG cc_start: 0.6901 (tpt90) cc_final: 0.6564 (tpt90) REVERT: A 1899 HIS cc_start: 0.7342 (m-70) cc_final: 0.6932 (t-90) REVERT: A 2025 GLU cc_start: 0.8354 (pt0) cc_final: 0.7964 (pm20) outliers start: 40 outliers final: 25 residues processed: 199 average time/residue: 0.2977 time to fit residues: 88.9805 Evaluate side-chains 190 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2067 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 40.0000 chunk 87 optimal weight: 0.0070 chunk 122 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16078 Z= 0.174 Angle : 0.675 9.792 21836 Z= 0.327 Chirality : 0.045 0.368 2539 Planarity : 0.004 0.059 2744 Dihedral : 11.983 114.823 2609 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.88 % Favored : 88.87 % Rotamer: Outliers : 2.89 % Allowed : 13.52 % Favored : 83.58 % 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: -2.65 (0.19), residues: 1985 helix: -0.60 (0.18), residues: 934 sheet: -1.26 (0.38), residues: 186 loop : -3.26 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 605 HIS 0.005 0.001 HIS A1941 PHE 0.026 0.001 PHE A1146 TYR 0.018 0.001 TYR A 340 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 677 GLU cc_start: 0.8225 (pp20) cc_final: 0.7831 (tt0) REVERT: A 992 ARG cc_start: 0.7433 (ptt180) cc_final: 0.7083 (ptt90) REVERT: A 1155 LEU cc_start: 0.8261 (mp) cc_final: 0.8042 (mp) REVERT: A 1241 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7310 (mtm-85) REVERT: A 1276 VAL cc_start: 0.8265 (t) cc_final: 0.7995 (t) REVERT: A 1419 MET cc_start: 0.8558 (tpt) cc_final: 0.8128 (tpt) REVERT: A 1493 ARG cc_start: 0.6774 (tpt90) cc_final: 0.6547 (tpt90) REVERT: A 1899 HIS cc_start: 0.7368 (m-70) cc_final: 0.6859 (t-90) REVERT: A 2025 GLU cc_start: 0.8277 (pt0) cc_final: 0.7903 (pm20) outliers start: 46 outliers final: 29 residues processed: 223 average time/residue: 0.3036 time to fit residues: 102.6480 Evaluate side-chains 195 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1614 ASN Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1933 ASN Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1871 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16078 Z= 0.280 Angle : 0.721 10.019 21836 Z= 0.349 Chirality : 0.048 0.336 2539 Planarity : 0.004 0.056 2744 Dihedral : 11.586 114.857 2603 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.79 % Favored : 88.01 % Rotamer: Outliers : 3.27 % Allowed : 15.09 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.19), residues: 1985 helix: -0.56 (0.18), residues: 939 sheet: -1.45 (0.39), residues: 183 loop : -3.16 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 605 HIS 0.006 0.001 HIS A1941 PHE 0.019 0.001 PHE A1416 TYR 0.024 0.002 TYR A 400 ARG 0.004 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7787 (tp40) REVERT: A 304 MET cc_start: 0.5454 (ppp) cc_final: 0.5195 (ppp) REVERT: A 322 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9016 (tp) REVERT: A 727 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7342 (p90) REVERT: A 992 ARG cc_start: 0.7496 (ptt180) cc_final: 0.7160 (ptt90) REVERT: A 1202 ASP cc_start: 0.5604 (OUTLIER) cc_final: 0.5169 (m-30) REVERT: A 1241 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7334 (mtm-85) REVERT: A 1276 VAL cc_start: 0.8267 (t) cc_final: 0.7957 (t) REVERT: A 1493 ARG cc_start: 0.6795 (tpt90) cc_final: 0.6498 (tpt90) REVERT: A 1899 HIS cc_start: 0.7362 (m-70) cc_final: 0.6946 (t-90) REVERT: A 2025 GLU cc_start: 0.8298 (pt0) cc_final: 0.7845 (pm20) REVERT: A 2189 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6225 (m-10) outliers start: 52 outliers final: 34 residues processed: 217 average time/residue: 0.2959 time to fit residues: 96.6582 Evaluate side-chains 212 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1491 SER Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1614 ASN Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1933 ASN Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 0.5980 chunk 174 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 50.0000 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16078 Z= 0.191 Angle : 0.674 9.789 21836 Z= 0.326 Chirality : 0.045 0.321 2539 Planarity : 0.004 0.057 2744 Dihedral : 11.115 113.784 2603 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.13 % Favored : 88.61 % Rotamer: Outliers : 3.21 % Allowed : 15.97 % Favored : 80.82 % 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: -2.37 (0.19), residues: 1985 helix: -0.39 (0.18), residues: 944 sheet: -1.08 (0.39), residues: 187 loop : -3.12 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 605 HIS 0.003 0.001 HIS A1941 PHE 0.032 0.001 PHE A1146 TYR 0.017 0.001 TYR A 345 ARG 0.005 0.000 ARG A1161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 182 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7830 (tp40) REVERT: A 677 GLU cc_start: 0.8213 (pp20) cc_final: 0.7837 (tt0) REVERT: A 727 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7454 (p90) REVERT: A 992 ARG cc_start: 0.7430 (ptt180) cc_final: 0.7045 (ptt90) REVERT: A 1161 ARG cc_start: 0.7607 (mtm180) cc_final: 0.7279 (mtm180) REVERT: A 1202 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.5533 (m-30) REVERT: A 1241 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7267 (mtm-85) REVERT: A 1276 VAL cc_start: 0.8233 (t) cc_final: 0.7959 (t) REVERT: A 1419 MET cc_start: 0.8456 (tpp) cc_final: 0.7956 (tpt) REVERT: A 1493 ARG cc_start: 0.6692 (tpt90) cc_final: 0.6413 (tpt90) REVERT: A 1871 HIS cc_start: 0.7364 (t-90) cc_final: 0.7135 (t-90) REVERT: A 1899 HIS cc_start: 0.7370 (m-70) cc_final: 0.6838 (t-90) REVERT: A 2025 GLU cc_start: 0.8268 (pt0) cc_final: 0.7841 (pm20) REVERT: A 2189 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6141 (m-10) REVERT: A 2209 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7063 (tm-30) outliers start: 51 outliers final: 36 residues processed: 216 average time/residue: 0.2886 time to fit residues: 95.4795 Evaluate side-chains 211 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1491 SER Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1614 ASN Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 110 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 118 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1933 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16078 Z= 0.167 Angle : 0.655 9.680 21836 Z= 0.315 Chirality : 0.044 0.325 2539 Planarity : 0.004 0.057 2744 Dihedral : 10.627 112.802 2603 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.88 % Favored : 88.87 % Rotamer: Outliers : 3.02 % Allowed : 16.54 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.19), residues: 1985 helix: -0.22 (0.18), residues: 941 sheet: -0.88 (0.39), residues: 186 loop : -3.07 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 605 HIS 0.003 0.001 HIS A1941 PHE 0.020 0.001 PHE A1146 TYR 0.016 0.001 TYR A 345 ARG 0.004 0.000 ARG A1161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 194 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7781 (tp40) REVERT: A 304 MET cc_start: 0.5486 (ppp) cc_final: 0.5083 (ppp) REVERT: A 677 GLU cc_start: 0.8182 (pp20) cc_final: 0.7861 (tt0) REVERT: A 727 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7417 (p90) REVERT: A 992 ARG cc_start: 0.7410 (ptt180) cc_final: 0.7199 (ptt90) REVERT: A 1030 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8923 (tt) REVERT: A 1161 ARG cc_start: 0.7597 (mtm180) cc_final: 0.7223 (mtm180) REVERT: A 1276 VAL cc_start: 0.8246 (t) cc_final: 0.7982 (t) REVERT: A 1414 TYR cc_start: 0.7912 (m-80) cc_final: 0.7679 (m-80) REVERT: A 1419 MET cc_start: 0.8437 (tpp) cc_final: 0.7883 (tpt) REVERT: A 1491 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8535 (p) REVERT: A 1493 ARG cc_start: 0.6653 (tpt90) cc_final: 0.6416 (tpt90) REVERT: A 1601 GLU cc_start: 0.7511 (pp20) cc_final: 0.6466 (pp20) REVERT: A 1899 HIS cc_start: 0.7465 (m-70) cc_final: 0.6900 (t-90) REVERT: A 2025 GLU cc_start: 0.8230 (pt0) cc_final: 0.7815 (pm20) REVERT: A 2130 MET cc_start: 0.8544 (mmp) cc_final: 0.8330 (mmp) REVERT: A 2189 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.6088 (m-10) REVERT: A 2209 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7266 (tm-30) outliers start: 48 outliers final: 37 residues processed: 229 average time/residue: 0.2740 time to fit residues: 95.2684 Evaluate side-chains 219 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 177 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1491 SER Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2031 GLU Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 18 optimal weight: 0.0470 chunk 152 optimal weight: 0.9990 chunk 176 optimal weight: 0.0970 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1871 HIS A2155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16078 Z= 0.157 Angle : 0.665 12.327 21836 Z= 0.318 Chirality : 0.045 0.320 2539 Planarity : 0.004 0.055 2744 Dihedral : 10.463 111.317 2597 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.43 % Favored : 89.42 % Rotamer: Outliers : 2.70 % Allowed : 17.67 % Favored : 79.62 % 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: -2.05 (0.19), residues: 1985 helix: -0.10 (0.18), residues: 946 sheet: -0.75 (0.41), residues: 178 loop : -3.02 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 605 HIS 0.006 0.001 HIS A 289 PHE 0.024 0.001 PHE A1146 TYR 0.017 0.001 TYR A 340 ARG 0.006 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7698 (tp40) REVERT: A 304 MET cc_start: 0.5377 (ppp) cc_final: 0.5001 (ppp) REVERT: A 677 GLU cc_start: 0.8127 (pp20) cc_final: 0.7855 (tt0) REVERT: A 727 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.7343 (p90) REVERT: A 992 ARG cc_start: 0.7390 (ptt180) cc_final: 0.7167 (ptt90) REVERT: A 1030 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8898 (tt) REVERT: A 1161 ARG cc_start: 0.7485 (mtm180) cc_final: 0.7250 (mtm180) REVERT: A 1202 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5271 (m-30) REVERT: A 1276 VAL cc_start: 0.8166 (t) cc_final: 0.7894 (t) REVERT: A 1419 MET cc_start: 0.8448 (tpp) cc_final: 0.7865 (tpt) REVERT: A 1491 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8490 (p) REVERT: A 1493 ARG cc_start: 0.6685 (tpt90) cc_final: 0.6460 (tpt90) REVERT: A 1601 GLU cc_start: 0.7245 (pp20) cc_final: 0.6273 (pp20) REVERT: A 1899 HIS cc_start: 0.7283 (m-70) cc_final: 0.6887 (t-90) REVERT: A 2025 GLU cc_start: 0.8221 (pt0) cc_final: 0.7814 (pm20) REVERT: A 2102 ASP cc_start: 0.7123 (m-30) cc_final: 0.6825 (p0) REVERT: A 2108 MET cc_start: 0.7612 (mmm) cc_final: 0.7390 (mmp) REVERT: A 2130 MET cc_start: 0.8518 (mmp) cc_final: 0.8316 (mmp) REVERT: A 2189 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.6201 (m-10) REVERT: A 2209 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 2222 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7685 (pp) outliers start: 43 outliers final: 31 residues processed: 225 average time/residue: 0.2865 time to fit residues: 97.9041 Evaluate side-chains 217 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 179 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1491 SER Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Chi-restraints excluded: chain A residue 2222 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 180 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 179 optimal weight: 0.0010 chunk 118 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16078 Z= 0.162 Angle : 0.651 9.651 21836 Z= 0.311 Chirality : 0.044 0.324 2539 Planarity : 0.004 0.055 2744 Dihedral : 10.478 110.585 2597 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.58 % Favored : 89.27 % Rotamer: Outliers : 2.96 % Allowed : 17.55 % Favored : 79.50 % 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: -1.96 (0.19), residues: 1985 helix: -0.02 (0.18), residues: 946 sheet: -0.66 (0.41), residues: 178 loop : -3.01 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 298 HIS 0.005 0.001 HIS A 289 PHE 0.018 0.001 PHE A1363 TYR 0.016 0.001 TYR A 345 ARG 0.005 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 187 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7761 (tp40) REVERT: A 280 MET cc_start: 0.5681 (mmt) cc_final: 0.5320 (mmp) REVERT: A 298 TRP cc_start: 0.7836 (t-100) cc_final: 0.7368 (t-100) REVERT: A 304 MET cc_start: 0.5469 (ppp) cc_final: 0.5064 (ppp) REVERT: A 677 GLU cc_start: 0.8127 (pp20) cc_final: 0.7856 (tt0) REVERT: A 727 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7317 (p90) REVERT: A 795 SER cc_start: 0.9087 (p) cc_final: 0.8707 (m) REVERT: A 992 ARG cc_start: 0.7367 (ptt180) cc_final: 0.7106 (ptt90) REVERT: A 1030 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8912 (tt) REVERT: A 1161 ARG cc_start: 0.7464 (mtm180) cc_final: 0.7186 (mtm180) REVERT: A 1276 VAL cc_start: 0.8169 (t) cc_final: 0.7898 (t) REVERT: A 1373 PHE cc_start: 0.7837 (t80) cc_final: 0.7465 (t80) REVERT: A 1419 MET cc_start: 0.8566 (tpp) cc_final: 0.7988 (tpt) REVERT: A 1601 GLU cc_start: 0.7048 (pp20) cc_final: 0.6229 (pp20) REVERT: A 1899 HIS cc_start: 0.7287 (m-70) cc_final: 0.6882 (t-90) REVERT: A 2025 GLU cc_start: 0.8212 (pt0) cc_final: 0.7810 (pm20) REVERT: A 2102 ASP cc_start: 0.7183 (m-30) cc_final: 0.6741 (p0) REVERT: A 2189 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6178 (m-10) REVERT: A 2209 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7339 (tm-30) outliers start: 47 outliers final: 37 residues processed: 222 average time/residue: 0.2786 time to fit residues: 94.5752 Evaluate side-chains 221 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2031 GLU Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 123 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 126 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16078 Z= 0.159 Angle : 0.659 10.678 21836 Z= 0.315 Chirality : 0.045 0.395 2539 Planarity : 0.004 0.053 2744 Dihedral : 9.899 109.802 2597 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.58 % Favored : 89.32 % Rotamer: Outliers : 2.64 % Allowed : 17.92 % Favored : 79.43 % 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: -1.88 (0.19), residues: 1985 helix: 0.06 (0.18), residues: 942 sheet: -0.55 (0.41), residues: 178 loop : -2.99 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 605 HIS 0.005 0.001 HIS A 289 PHE 0.025 0.001 PHE A 503 TYR 0.016 0.001 TYR A 345 ARG 0.005 0.000 ARG A 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 182 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7667 (tp40) REVERT: A 280 MET cc_start: 0.5639 (mmt) cc_final: 0.5334 (mmp) REVERT: A 304 MET cc_start: 0.5394 (ppp) cc_final: 0.5014 (ppp) REVERT: A 677 GLU cc_start: 0.8134 (pp20) cc_final: 0.7887 (tt0) REVERT: A 727 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7282 (p90) REVERT: A 795 SER cc_start: 0.9099 (p) cc_final: 0.8750 (m) REVERT: A 992 ARG cc_start: 0.7358 (ptt180) cc_final: 0.7098 (ptt90) REVERT: A 1030 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8906 (tt) REVERT: A 1161 ARG cc_start: 0.7411 (mtm180) cc_final: 0.7109 (mtm180) REVERT: A 1276 VAL cc_start: 0.8159 (t) cc_final: 0.7898 (t) REVERT: A 1373 PHE cc_start: 0.7849 (t80) cc_final: 0.7491 (t80) REVERT: A 1419 MET cc_start: 0.8566 (tpp) cc_final: 0.7968 (tpt) REVERT: A 1548 SER cc_start: 0.7312 (t) cc_final: 0.7062 (p) REVERT: A 1601 GLU cc_start: 0.7030 (pp20) cc_final: 0.6258 (pp20) REVERT: A 2025 GLU cc_start: 0.8248 (pt0) cc_final: 0.7863 (pm20) REVERT: A 2102 ASP cc_start: 0.7017 (m-30) cc_final: 0.6787 (p0) REVERT: A 2189 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.6171 (m-10) REVERT: A 2209 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7370 (tm-30) outliers start: 42 outliers final: 36 residues processed: 214 average time/residue: 0.2841 time to fit residues: 92.8851 Evaluate side-chains 219 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1614 ASN Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2031 GLU Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 66 optimal weight: 0.0020 chunk 163 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 29 optimal weight: 0.0050 chunk 140 optimal weight: 2.9990 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 GLN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.151436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115729 restraints weight = 23718.825| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.47 r_work: 0.3118 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16078 Z= 0.160 Angle : 0.654 9.973 21836 Z= 0.311 Chirality : 0.045 0.351 2539 Planarity : 0.004 0.053 2744 Dihedral : 9.626 108.963 2597 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.78 % Favored : 89.12 % Rotamer: Outliers : 2.83 % Allowed : 18.11 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.19), residues: 1985 helix: 0.17 (0.18), residues: 944 sheet: -0.52 (0.41), residues: 183 loop : -2.96 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 298 HIS 0.005 0.000 HIS A 289 PHE 0.016 0.001 PHE A1363 TYR 0.016 0.001 TYR A 345 ARG 0.006 0.000 ARG A2139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3305.36 seconds wall clock time: 61 minutes 13.70 seconds (3673.70 seconds total)