Starting phenix.real_space_refine on Sun Feb 18 23:23:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whs_21674/02_2024/6whs_21674.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whs_21674/02_2024/6whs_21674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whs_21674/02_2024/6whs_21674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whs_21674/02_2024/6whs_21674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whs_21674/02_2024/6whs_21674.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whs_21674/02_2024/6whs_21674.pdb" } resolution = 4.0 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= 0.008 sd= 0.725 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 298 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 14694 2.51 5 N 3730 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 543": "OE1" <-> "OE2" Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A GLU 832": "OE1" <-> "OE2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B GLU 552": "OE1" <-> "OE2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "B ARG 742": "NH1" <-> "NH2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 822": "NH1" <-> "NH2" Residue "C GLU 832": "OE1" <-> "OE2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D GLU 552": "OE1" <-> "OE2" Residue "D GLU 692": "OE1" <-> "OE2" Residue "D ARG 742": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22866 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 5705 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 35, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 733 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 395 Chain: "B" Number of atoms: 5644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5644 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 27, 'TRANS': 759} Chain breaks: 2 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 713 Unresolved non-hydrogen dihedrals: 524 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 14, 'TYR:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 32, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 383 Chain: "C" Number of atoms: 5705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 5705 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 35, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 733 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 395 Chain: "D" Number of atoms: 5644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5644 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 27, 'TRANS': 759} Chain breaks: 2 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 713 Unresolved non-hydrogen dihedrals: 524 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 14, 'TYR:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 32, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 383 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.95, per 1000 atoms: 0.52 Number of scatterers: 22866 At special positions: 0 Unit cell: (138.37, 154.81, 179.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4332 8.00 N 3730 7.00 C 14694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.06 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.02 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.06 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.04 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.04 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.02 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 224 " " NAG A1002 " - " ASN A 297 " " NAG B 903 " - " ASN B 491 " " NAG B 904 " - " ASN B 341 " " NAG C1001 " - " ASN C 224 " " NAG C1002 " - " ASN C 297 " " NAG D 903 " - " ASN D 491 " " NAG D 904 " - " ASN D 341 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Time building additional restraints: 9.45 Conformation dependent library (CDL) restraints added in 4.8 seconds 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5924 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 38 sheets defined 43.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.717A pdb=" N MET A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.562A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.793A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.909A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.889A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.979A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.528A pdb=" N ALA A 279 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.582A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 480 through 492 Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.845A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 580 through 604 removed outlier: 3.530A pdb=" N TRP A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.905A pdb=" N TRP A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.813A pdb=" N LEU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.782A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.987A pdb=" N LYS A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.592A pdb=" N ASP A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.764A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 862 removed outlier: 4.053A pdb=" N MET A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 106 through 119 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.761A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.877A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.575A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 235 through 246 removed outlier: 4.417A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 289 through 311 removed outlier: 3.937A pdb=" N VAL B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 removed outlier: 4.045A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.610A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 580 removed outlier: 3.612A pdb=" N MET B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.982A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.667A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 674 through 677 Processing helix chain 'B' and resid 689 through 696 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 771 through 786 removed outlier: 3.845A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 779 " --> pdb=" O GLN B 775 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 814 through 844 removed outlier: 4.469A pdb=" N MET B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.718A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.561A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.793A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.910A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 158 removed outlier: 3.889A pdb=" N MET C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 225 through 235 removed outlier: 3.979A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.527A pdb=" N ALA C 279 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.582A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 480 through 492 Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.845A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 580 through 604 removed outlier: 3.530A pdb=" N TRP C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.905A pdb=" N TRP C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 676 removed outlier: 3.813A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.782A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.985A pdb=" N LYS C 729 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.593A pdb=" N ASP C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.764A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 803 Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 862 removed outlier: 4.052A pdb=" N MET C 834 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY C 836 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 851 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG C 860 " --> pdb=" O ILE C 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 106 through 119 Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.761A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.877A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.577A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 235 through 246 removed outlier: 4.417A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 283 through 288 Processing helix chain 'D' and resid 289 through 311 removed outlier: 3.936A pdb=" N VAL D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 removed outlier: 4.045A pdb=" N ILE D 340 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.610A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 580 removed outlier: 3.611A pdb=" N MET D 561 " --> pdb=" O CYS D 557 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 571 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.982A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.666A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 634 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP D 635 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 644 " --> pdb=" O VAL D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 674 through 677 Processing helix chain 'D' and resid 689 through 696 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 771 through 786 removed outlier: 3.845A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 779 " --> pdb=" O GLN D 775 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 814 through 844 removed outlier: 4.470A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 819 " --> pdb=" O ILE D 815 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 9.141A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 218 removed outlier: 7.379A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 218 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 167 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 168 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 292 removed outlier: 5.935A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN A 378 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.093A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 7.657A pdb=" N LEU A 419 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N HIS A 498 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 511 removed outlier: 4.590A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 549 through 550 Processing sheet with id=AA9, first strand: chain 'A' and resid 555 through 557 Processing sheet with id=AB1, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AB2, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.511A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.845A pdb=" N PHE B 169 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.845A pdb=" N PHE B 169 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB6, first strand: chain 'B' and resid 405 through 409 removed outlier: 6.797A pdb=" N LEU B 406 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR B 479 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 478 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB8, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC1, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.687A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 59 through 65 removed outlier: 9.141A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 215 through 218 removed outlier: 7.379A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE C 218 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL C 167 " --> pdb=" O PHE C 218 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 168 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 288 through 292 removed outlier: 5.935A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN C 378 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU C 382 " --> pdb=" O GLN C 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.093A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 418 through 423 removed outlier: 7.657A pdb=" N LEU C 419 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N HIS C 498 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 430 through 434 Processing sheet with id=AC8, first strand: chain 'C' and resid 508 through 511 removed outlier: 4.590A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 549 through 550 Processing sheet with id=AD1, first strand: chain 'C' and resid 555 through 557 Processing sheet with id=AD2, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AD3, first strand: chain 'D' and resid 67 through 71 removed outlier: 3.511A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.845A pdb=" N PHE D 169 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.845A pdb=" N PHE D 169 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD7, first strand: chain 'D' and resid 405 through 409 removed outlier: 6.798A pdb=" N LEU D 406 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR D 479 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU D 478 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD9, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AE1, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AE2, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.688A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2946 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: 8.88 Time building geometry restraints manager: 9.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7419 1.35 - 1.48: 6118 1.48 - 1.60: 9641 1.60 - 1.73: 0 1.73 - 1.86: 178 Bond restraints: 23356 Sorted by residual: bond pdb=" CA ARG D 696 " pdb=" C ARG D 696 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.34e-02 5.57e+03 2.12e+01 bond pdb=" CA ARG B 696 " pdb=" C ARG B 696 " ideal model delta sigma weight residual 1.523 1.462 0.062 1.34e-02 5.57e+03 2.12e+01 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 NAG B 903 " pdb=" O5 NAG B 903 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" CA LEU A 676 " pdb=" C LEU A 676 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.80e-02 3.09e+03 6.05e+00 ... (remaining 23351 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.77: 427 104.77 - 112.11: 12518 112.11 - 119.46: 7136 119.46 - 126.80: 11631 126.80 - 134.14: 310 Bond angle restraints: 32022 Sorted by residual: angle pdb=" N GLU C 682 " pdb=" CA GLU C 682 " pdb=" C GLU C 682 " ideal model delta sigma weight residual 111.71 118.78 -7.07 1.15e+00 7.56e-01 3.78e+01 angle pdb=" N GLU A 682 " pdb=" CA GLU A 682 " pdb=" C GLU A 682 " ideal model delta sigma weight residual 111.71 118.74 -7.03 1.15e+00 7.56e-01 3.73e+01 angle pdb=" C ILE C 688 " pdb=" CA ILE C 688 " pdb=" CB ILE C 688 " ideal model delta sigma weight residual 111.29 102.22 9.07 1.64e+00 3.72e-01 3.06e+01 angle pdb=" C ILE A 688 " pdb=" CA ILE A 688 " pdb=" CB ILE A 688 " ideal model delta sigma weight residual 111.29 102.31 8.98 1.64e+00 3.72e-01 3.00e+01 angle pdb=" CA LEU A 676 " pdb=" C LEU A 676 " pdb=" N VAL A 677 " ideal model delta sigma weight residual 118.27 126.46 -8.19 1.59e+00 3.96e-01 2.65e+01 ... (remaining 32017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 13019 23.85 - 47.70: 677 47.70 - 71.55: 64 71.55 - 95.40: 18 95.40 - 119.25: 6 Dihedral angle restraints: 13784 sinusoidal: 4606 harmonic: 9178 Sorted by residual: dihedral pdb=" CA GLU C 682 " pdb=" C GLU C 682 " pdb=" N GLU C 683 " pdb=" CA GLU C 683 " ideal model delta harmonic sigma weight residual -180.00 -131.65 -48.35 0 5.00e+00 4.00e-02 9.35e+01 dihedral pdb=" CA GLU A 682 " pdb=" C GLU A 682 " pdb=" N GLU A 683 " pdb=" CA GLU A 683 " ideal model delta harmonic sigma weight residual -180.00 -131.67 -48.33 0 5.00e+00 4.00e-02 9.34e+01 dihedral pdb=" CB CYS C 457 " pdb=" SG CYS C 457 " pdb=" SG CYS C 476 " pdb=" CB CYS C 476 " ideal model delta sinusoidal sigma weight residual -86.00 -166.39 80.39 1 1.00e+01 1.00e-02 8.00e+01 ... (remaining 13781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3514 0.083 - 0.167: 387 0.167 - 0.250: 13 0.250 - 0.334: 0 0.334 - 0.417: 2 Chirality restraints: 3916 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.36e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.31e+02 chirality pdb=" CB ILE A 688 " pdb=" CA ILE A 688 " pdb=" CG1 ILE A 688 " pdb=" CG2 ILE A 688 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3913 not shown) Planarity restraints: 4082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 680 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO C 681 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 681 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 681 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 680 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO A 681 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 105 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO C 106 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " 0.037 5.00e-02 4.00e+02 ... (remaining 4079 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 694 2.65 - 3.21: 25238 3.21 - 3.78: 33832 3.78 - 4.34: 42339 4.34 - 4.90: 67124 Nonbonded interactions: 169227 Sorted by model distance: nonbonded pdb=" O LEU D 567 " pdb=" OG SER D 570 " model vdw 2.088 2.440 nonbonded pdb=" O LEU B 567 " pdb=" OG SER B 570 " model vdw 2.088 2.440 nonbonded pdb=" O PHE A 102 " pdb=" OG1 THR A 105 " model vdw 2.116 2.440 nonbonded pdb=" O PHE C 102 " pdb=" OG1 THR C 105 " model vdw 2.117 2.440 nonbonded pdb=" OG1 THR B 410 " pdb=" N LEU B 411 " model vdw 2.131 2.520 ... (remaining 169222 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 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 5.110 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 62.550 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.160 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.010 0.079 23356 Z= 0.653 Angle : 0.938 11.390 32022 Z= 0.513 Chirality : 0.051 0.417 3916 Planarity : 0.006 0.070 4072 Dihedral : 14.542 119.249 7812 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.63 % Favored : 83.37 % Rotamer: Outliers : 0.82 % Allowed : 14.22 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.33 % 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: -4.97 (0.12), residues: 3144 helix: -2.67 (0.11), residues: 1212 sheet: -3.46 (0.22), residues: 378 loop : -3.83 (0.13), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 772 HIS 0.007 0.002 HIS B 703 PHE 0.023 0.003 PHE C 550 TYR 0.034 0.002 TYR B 731 ARG 0.006 0.001 ARG D 742 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 230 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 GLU cc_start: 0.5064 (pp20) cc_final: 0.4220 (mp0) REVERT: A 688 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 727 MET cc_start: 0.7051 (ttm) cc_final: 0.6834 (ttm) REVERT: B 410 THR cc_start: 0.9531 (OUTLIER) cc_final: 0.9291 (p) REVERT: C 727 MET cc_start: 0.7200 (ttm) cc_final: 0.6971 (ttm) REVERT: D 160 ILE cc_start: 0.8906 (tt) cc_final: 0.8683 (tt) outliers start: 18 outliers final: 8 residues processed: 246 average time/residue: 0.2744 time to fit residues: 114.5711 Evaluate side-chains 182 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain D residue 410 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 30.0000 chunk 237 optimal weight: 0.0270 chunk 132 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 160 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 246 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 285 optimal weight: 0.9980 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 162 HIS A 171 HIS A 177 GLN A 217 GLN A 294 ASN A 530 GLN A 695 ASN A 731 ASN A 801 HIS ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN B 368 ASN B 486 HIS B 656 GLN B 697 ASN C 47 ASN C 162 HIS C 171 HIS C 177 GLN C 217 GLN C 294 ASN C 530 GLN C 695 ASN C 731 ASN C 801 HIS ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN D 368 ASN D 486 HIS D 656 GLN D 697 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 23356 Z= 0.305 Angle : 0.705 7.938 32022 Z= 0.371 Chirality : 0.046 0.312 3916 Planarity : 0.005 0.064 4072 Dihedral : 8.346 103.450 3577 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 2.96 % Allowed : 18.46 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.20 % 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: -3.53 (0.13), residues: 3144 helix: -1.03 (0.13), residues: 1250 sheet: -2.87 (0.23), residues: 366 loop : -3.42 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 789 HIS 0.004 0.001 HIS A 146 PHE 0.018 0.002 PHE B 642 TYR 0.017 0.002 TYR A 388 ARG 0.003 0.000 ARG C 822 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 206 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 GLU cc_start: 0.4850 (pp20) cc_final: 0.4199 (mp0) REVERT: B 358 MET cc_start: 0.8421 (ppp) cc_final: 0.7923 (ppp) REVERT: B 653 PHE cc_start: 0.7612 (t80) cc_final: 0.7383 (t80) REVERT: B 732 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.5997 (m-30) REVERT: C 458 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8869 (p) REVERT: D 160 ILE cc_start: 0.8905 (tt) cc_final: 0.8668 (tt) REVERT: D 732 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6153 (m-30) outliers start: 65 outliers final: 40 residues processed: 257 average time/residue: 0.2719 time to fit residues: 122.3456 Evaluate side-chains 224 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 181 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 285 optimal weight: 6.9990 chunk 308 optimal weight: 0.7980 chunk 254 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 229 optimal weight: 0.5980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23356 Z= 0.244 Angle : 0.649 9.893 32022 Z= 0.339 Chirality : 0.045 0.316 3916 Planarity : 0.004 0.060 4072 Dihedral : 7.736 99.541 3572 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 4.06 % Allowed : 19.69 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.20 % 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: -2.73 (0.14), residues: 3144 helix: -0.13 (0.14), residues: 1226 sheet: -2.66 (0.24), residues: 358 loop : -3.12 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 772 HIS 0.012 0.001 HIS A 801 PHE 0.022 0.002 PHE D 653 TYR 0.018 0.001 TYR D 282 ARG 0.003 0.000 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 199 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 358 MET cc_start: 0.8379 (ppp) cc_final: 0.7991 (ppp) REVERT: B 732 ASP cc_start: 0.6712 (OUTLIER) cc_final: 0.5847 (m-30) REVERT: B 806 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7275 (p0) REVERT: C 458 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8922 (p) REVERT: D 732 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.5981 (m-30) outliers start: 89 outliers final: 54 residues processed: 264 average time/residue: 0.2624 time to fit residues: 121.3028 Evaluate side-chains 241 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 183 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 191 optimal weight: 0.0970 chunk 286 optimal weight: 10.0000 chunk 303 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 731 ASN A 801 HIS A 824 ASN B 385 GLN C 134 HIS C 731 ASN ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23356 Z= 0.161 Angle : 0.611 11.782 32022 Z= 0.315 Chirality : 0.044 0.359 3916 Planarity : 0.004 0.057 4072 Dihedral : 7.194 96.347 3571 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.60 % Allowed : 22.06 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.07 % 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: -2.15 (0.15), residues: 3144 helix: 0.35 (0.15), residues: 1240 sheet: -2.13 (0.25), residues: 374 loop : -2.86 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 635 HIS 0.014 0.001 HIS A 801 PHE 0.023 0.001 PHE D 653 TYR 0.018 0.001 TYR B 282 ARG 0.002 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 208 time to evaluate : 2.593 Fit side-chains REVERT: B 157 MET cc_start: 0.5948 (ptm) cc_final: 0.5206 (ttt) REVERT: B 358 MET cc_start: 0.8278 (ppp) cc_final: 0.7974 (ppp) REVERT: B 551 LEU cc_start: 0.7973 (mt) cc_final: 0.7757 (mt) REVERT: B 806 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.7130 (p0) REVERT: C 230 MET cc_start: 0.5415 (mmm) cc_final: 0.4933 (mmp) REVERT: C 458 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8851 (p) outliers start: 79 outliers final: 49 residues processed: 267 average time/residue: 0.2524 time to fit residues: 118.9455 Evaluate side-chains 245 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 194 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 76 optimal weight: 0.0070 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN C 731 ASN ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23356 Z= 0.298 Angle : 0.656 13.024 32022 Z= 0.339 Chirality : 0.045 0.387 3916 Planarity : 0.004 0.057 4072 Dihedral : 7.100 92.388 3571 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 4.74 % Allowed : 22.47 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.06 (0.15), residues: 3144 helix: 0.47 (0.15), residues: 1234 sheet: -2.42 (0.24), residues: 398 loop : -2.73 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 635 HIS 0.006 0.001 HIS A 801 PHE 0.026 0.002 PHE D 653 TYR 0.017 0.001 TYR D 282 ARG 0.002 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 198 time to evaluate : 2.965 Fit side-chains REVERT: B 358 MET cc_start: 0.8297 (ppp) cc_final: 0.8042 (ppp) REVERT: B 732 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.6001 (m-30) REVERT: B 806 ASN cc_start: 0.7361 (OUTLIER) cc_final: 0.7094 (p0) REVERT: C 230 MET cc_start: 0.5398 (mmm) cc_final: 0.4962 (mmm) REVERT: C 458 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8890 (p) REVERT: D 732 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6056 (m-30) outliers start: 104 outliers final: 70 residues processed: 279 average time/residue: 0.2550 time to fit residues: 125.2478 Evaluate side-chains 261 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 187 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 178 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 303 optimal weight: 0.8980 chunk 252 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 159 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 824 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 23356 Z= 0.162 Angle : 0.608 14.031 32022 Z= 0.310 Chirality : 0.044 0.376 3916 Planarity : 0.004 0.055 4072 Dihedral : 6.735 89.508 3570 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.01 % Allowed : 23.34 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.15), residues: 3144 helix: 0.62 (0.15), residues: 1260 sheet: -2.30 (0.24), residues: 398 loop : -2.50 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 559 HIS 0.003 0.001 HIS A 301 PHE 0.031 0.001 PHE D 653 TYR 0.019 0.001 TYR B 282 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 212 time to evaluate : 2.498 Fit side-chains REVERT: C 230 MET cc_start: 0.5336 (mmm) cc_final: 0.5052 (mmm) outliers start: 88 outliers final: 63 residues processed: 280 average time/residue: 0.2507 time to fit residues: 123.3476 Evaluate side-chains 260 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 197 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 5.9990 chunk 34 optimal weight: 0.0980 chunk 173 optimal weight: 0.0570 chunk 221 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 184 optimal weight: 0.0030 chunk 139 optimal weight: 8.9990 overall best weight: 1.0310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 824 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 23356 Z= 0.166 Angle : 0.610 14.420 32022 Z= 0.307 Chirality : 0.044 0.409 3916 Planarity : 0.004 0.054 4072 Dihedral : 6.438 83.034 3570 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.69 % Allowed : 24.29 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.58 (0.15), residues: 3144 helix: 0.74 (0.15), residues: 1260 sheet: -2.12 (0.25), residues: 398 loop : -2.40 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 635 HIS 0.004 0.001 HIS C 592 PHE 0.028 0.001 PHE D 653 TYR 0.018 0.001 TYR B 282 ARG 0.001 0.000 ARG C 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 204 time to evaluate : 2.760 Fit side-chains REVERT: C 230 MET cc_start: 0.5442 (mmm) cc_final: 0.5103 (mmm) REVERT: D 544 THR cc_start: 0.6620 (OUTLIER) cc_final: 0.6399 (p) REVERT: D 831 LEU cc_start: 0.6713 (pp) cc_final: 0.5959 (tt) outliers start: 81 outliers final: 69 residues processed: 268 average time/residue: 0.2598 time to fit residues: 122.7071 Evaluate side-chains 264 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 194 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 0.1980 chunk 120 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 206 optimal weight: 0.2980 chunk 149 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN C 159 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23356 Z= 0.286 Angle : 0.661 14.834 32022 Z= 0.335 Chirality : 0.044 0.406 3916 Planarity : 0.004 0.057 4072 Dihedral : 6.384 74.717 3570 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.19 % Allowed : 24.20 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.58 (0.15), residues: 3144 helix: 0.76 (0.15), residues: 1248 sheet: -2.16 (0.24), residues: 418 loop : -2.37 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 772 HIS 0.003 0.001 HIS A 801 PHE 0.030 0.002 PHE D 653 TYR 0.017 0.001 TYR B 282 ARG 0.002 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 190 time to evaluate : 2.735 Fit side-chains REVERT: C 230 MET cc_start: 0.5530 (mmm) cc_final: 0.5223 (mmm) outliers start: 92 outliers final: 76 residues processed: 263 average time/residue: 0.2609 time to fit residues: 120.6610 Evaluate side-chains 265 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 189 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 264 optimal weight: 0.0770 chunk 282 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 281 optimal weight: 0.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN C 217 GLN C 731 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23356 Z= 0.169 Angle : 0.631 15.016 32022 Z= 0.315 Chirality : 0.044 0.403 3916 Planarity : 0.004 0.055 4072 Dihedral : 6.117 67.532 3570 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.33 % Allowed : 25.25 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 3144 helix: 0.89 (0.15), residues: 1250 sheet: -2.07 (0.24), residues: 428 loop : -2.23 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 635 HIS 0.003 0.000 HIS C 301 PHE 0.031 0.001 PHE B 653 TYR 0.018 0.001 TYR B 282 ARG 0.001 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 198 time to evaluate : 2.668 Fit side-chains REVERT: B 806 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.6508 (p0) REVERT: D 558 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8386 (p) REVERT: D 654 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7139 (ttp) REVERT: D 831 LEU cc_start: 0.6753 (pp) cc_final: 0.5992 (tt) outliers start: 73 outliers final: 64 residues processed: 256 average time/residue: 0.2652 time to fit residues: 119.8835 Evaluate side-chains 261 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 194 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 192 optimal weight: 0.0670 chunk 152 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN C 671 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23356 Z= 0.166 Angle : 0.618 15.215 32022 Z= 0.307 Chirality : 0.043 0.420 3916 Planarity : 0.004 0.055 4072 Dihedral : 5.690 56.147 3570 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.10 % Allowed : 25.34 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.23 (0.15), residues: 3144 helix: 0.92 (0.15), residues: 1266 sheet: -1.84 (0.25), residues: 428 loop : -2.13 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 166 HIS 0.003 0.001 HIS C 301 PHE 0.033 0.001 PHE B 653 TYR 0.017 0.001 TYR D 282 ARG 0.001 0.000 ARG C 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 207 time to evaluate : 2.621 Fit side-chains REVERT: B 789 MET cc_start: 0.7867 (mmm) cc_final: 0.7646 (tpp) REVERT: D 654 MET cc_start: 0.7275 (ttm) cc_final: 0.6695 (ttp) REVERT: D 706 MET cc_start: 0.5819 (tpt) cc_final: 0.5384 (tpt) REVERT: D 789 MET cc_start: 0.7816 (mmm) cc_final: 0.7598 (tpp) REVERT: D 831 LEU cc_start: 0.6775 (pp) cc_final: 0.6029 (tt) outliers start: 68 outliers final: 65 residues processed: 261 average time/residue: 0.2539 time to fit residues: 116.3917 Evaluate side-chains 264 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 199 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 8.9990 chunk 265 optimal weight: 6.9990 chunk 76 optimal weight: 0.0770 chunk 229 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.092587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069843 restraints weight = 79574.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070661 restraints weight = 46919.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.071188 restraints weight = 34300.493| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23356 Z= 0.248 Angle : 0.655 15.087 32022 Z= 0.331 Chirality : 0.044 0.385 3916 Planarity : 0.004 0.055 4072 Dihedral : 5.695 59.494 3570 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.24 % Allowed : 25.48 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.24 (0.15), residues: 3144 helix: 0.91 (0.15), residues: 1264 sheet: -1.80 (0.25), residues: 418 loop : -2.14 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 166 HIS 0.003 0.001 HIS A 801 PHE 0.029 0.002 PHE D 653 TYR 0.017 0.001 TYR D 282 ARG 0.003 0.000 ARG C 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.98 seconds wall clock time: 70 minutes 22.57 seconds (4222.57 seconds total)