Starting phenix.real_space_refine (version: dev) on Thu Dec 15 01:10:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi1_21682/12_2022/6wi1_21682.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi1_21682/12_2022/6wi1_21682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi1_21682/12_2022/6wi1_21682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi1_21682/12_2022/6wi1_21682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi1_21682/12_2022/6wi1_21682.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi1_21682/12_2022/6wi1_21682.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 sd= 0.873 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 784": "NH1" <-> "NH2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 784": "NH1" <-> "NH2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D GLU 531": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 23366 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 5910 Classifications: {'peptide': 806} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 35, 'TRANS': 770} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 331 Chain: "B" Number of atoms: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5661 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 28, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 16, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 8, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 371 Chain: "C" Number of atoms: 5910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 5910 Classifications: {'peptide': 806} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 35, 'TRANS': 770} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 331 Chain: "D" Number of atoms: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5661 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 28, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 16, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 8, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 371 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 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "H" 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 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 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 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 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 chiralities: 2 Time building chain proxies: 12.65, per 1000 atoms: 0.54 Number of scatterers: 23366 At special positions: 0 Unit cell: (135.63, 149.33, 186.32, 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 130 16.00 O 4440 8.00 N 3856 7.00 C 14940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 719 " - pdb=" SG CYS B 795 " distance=2.00 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.05 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 719 " - pdb=" SG CYS D 795 " distance=2.09 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.05 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.05 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 901 " - " ASN A 224 " " NAG A 902 " - " ASN A 297 " " NAG B 903 " - " ASN B 491 " " NAG B 904 " - " ASN B 341 " " NAG C 901 " - " ASN C 224 " " NAG C 902 " - " 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 B 348 " " NAG G 1 " - " ASN D 688 " " NAG H 1 " - " ASN D 348 " Time building additional restraints: 10.08 Conformation dependent library (CDL) restraints added in 3.7 seconds 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 34 sheets defined 43.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.275A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.551A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.811A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.570A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.920A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 529 removed outlier: 4.149A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 581 through 605 removed outlier: 4.242A pdb=" N VAL A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 647 through 679 removed outlier: 4.044A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 787 through 803 removed outlier: 4.069A pdb=" N GLN A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 862 removed outlier: 4.449A pdb=" N GLY A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.723A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.948A pdb=" N ASP B 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS B 61 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 62 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 3.632A pdb=" N LYS B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.603A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.593A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 233 through 247 Processing helix chain 'B' and resid 288 through 312 removed outlier: 4.183A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.928A pdb=" N ILE B 329 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 removed outlier: 4.243A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.687A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.766A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.823A pdb=" N ALA B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 654 removed outlier: 4.016A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 714 through 724 removed outlier: 3.572A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.116A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.481A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 795 removed outlier: 3.585A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 844 removed outlier: 3.857A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 104 through 113 removed outlier: 4.274A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.552A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.811A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.570A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.921A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 520 through 529 removed outlier: 4.149A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 581 through 605 removed outlier: 4.242A pdb=" N VAL C 587 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 647 through 679 removed outlier: 4.046A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL C 677 " --> pdb=" O ALA C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing helix chain 'C' and resid 720 through 729 Processing helix chain 'C' and resid 734 through 744 Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 787 through 803 removed outlier: 4.070A pdb=" N GLN C 791 " --> pdb=" O SER C 787 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 862 removed outlier: 4.451A pdb=" N GLY C 836 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.723A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 62 removed outlier: 3.949A pdb=" N ASP D 58 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS D 60 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS D 61 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 62 " --> pdb=" O PHE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.632A pdb=" N LYS D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 150 through 164 removed outlier: 3.603A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.593A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 222 Processing helix chain 'D' and resid 233 through 247 Processing helix chain 'D' and resid 288 through 312 removed outlier: 4.183A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 331 removed outlier: 3.928A pdb=" N ILE D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 removed outlier: 4.243A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.687A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.767A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 578 Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.823A pdb=" N ALA D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 654 removed outlier: 4.016A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 690 through 699 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 714 through 724 removed outlier: 3.572A pdb=" N GLY D 724 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.117A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.481A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 795 removed outlier: 3.585A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 844 removed outlier: 3.858A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 61 removed outlier: 7.931A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 211 through 216 removed outlier: 7.505A pdb=" N ILE A 163 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 215 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 165 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A 239 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 269 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 242 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 292 removed outlier: 3.712A pdb=" N GLY A 386 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 431 through 434 removed outlier: 3.563A pdb=" N TYR A 477 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 456 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU A 499 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR A 458 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 Processing sheet with id=AA7, first strand: chain 'A' and resid 549 through 550 Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 703 removed outlier: 6.612A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 561 " --> pdb=" O THR A 770 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 73 removed outlier: 7.768A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 204 removed outlier: 6.281A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 170 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 230 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB4, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.621A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 728 through 732 removed outlier: 3.543A pdb=" N LEU B 748 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 728 through 732 removed outlier: 5.017A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 61 Processing sheet with id=AC1, first strand: chain 'C' and resid 59 through 61 removed outlier: 7.931A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 211 through 216 removed outlier: 7.505A pdb=" N ILE C 163 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 215 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 165 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL C 239 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 269 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 242 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 290 through 292 removed outlier: 3.711A pdb=" N GLY C 386 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 434 removed outlier: 3.563A pdb=" N TYR C 477 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 456 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU C 499 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR C 458 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 508 through 510 Processing sheet with id=AC6, first strand: chain 'C' and resid 549 through 550 Processing sheet with id=AC7, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AC8, first strand: chain 'C' and resid 702 through 703 removed outlier: 6.613A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 561 " --> pdb=" O THR C 770 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 73 removed outlier: 7.767A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 201 through 204 removed outlier: 6.281A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 170 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 230 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD3, first strand: chain 'D' and resid 408 through 409 Processing sheet with id=AD4, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.622A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD6, first strand: chain 'D' and resid 728 through 732 removed outlier: 3.544A pdb=" N LEU D 748 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 728 through 732 removed outlier: 5.016A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1074 hydrogen bonds defined for protein. 3102 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: 9.35 Time building geometry restraints manager: 10.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7574 1.34 - 1.47: 5765 1.47 - 1.59: 10295 1.59 - 1.71: 0 1.71 - 1.83: 216 Bond restraints: 23850 Sorted by residual: bond pdb=" C ILE A 401 " pdb=" N TRP A 402 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.86e-02 2.89e+03 9.07e+00 bond pdb=" C ILE C 401 " pdb=" N TRP C 402 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.86e-02 2.89e+03 8.93e+00 bond pdb=" CB TRP D 166 " pdb=" CG TRP D 166 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.43e+00 bond pdb=" CB TRP B 166 " pdb=" CG TRP B 166 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.34e+00 bond pdb=" CA PRO D 674 " pdb=" CB PRO D 674 " ideal model delta sigma weight residual 1.532 1.517 0.015 7.10e-03 1.98e+04 4.19e+00 ... (remaining 23845 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.68: 499 105.68 - 112.83: 13380 112.83 - 119.98: 7955 119.98 - 127.13: 10479 127.13 - 134.28: 269 Bond angle restraints: 32582 Sorted by residual: angle pdb=" C ILE D 85 " pdb=" N CYS D 86 " pdb=" CA CYS D 86 " ideal model delta sigma weight residual 121.14 111.58 9.56 1.75e+00 3.27e-01 2.98e+01 angle pdb=" C ILE B 85 " pdb=" N CYS B 86 " pdb=" CA CYS B 86 " ideal model delta sigma weight residual 121.14 111.58 9.56 1.75e+00 3.27e-01 2.98e+01 angle pdb=" CA CYS C 765 " pdb=" CB CYS C 765 " pdb=" SG CYS C 765 " ideal model delta sigma weight residual 114.40 126.66 -12.26 2.30e+00 1.89e-01 2.84e+01 angle pdb=" CA CYS A 765 " pdb=" CB CYS A 765 " pdb=" SG CYS A 765 " ideal model delta sigma weight residual 114.40 126.64 -12.24 2.30e+00 1.89e-01 2.83e+01 angle pdb=" C PRO A 468 " pdb=" N ARG A 469 " pdb=" CA ARG A 469 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 ... (remaining 32577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 12765 17.46 - 34.92: 1075 34.92 - 52.38: 166 52.38 - 69.83: 38 69.83 - 87.29: 18 Dihedral angle restraints: 14062 sinusoidal: 4864 harmonic: 9198 Sorted by residual: dihedral pdb=" CA LYS A 764 " pdb=" C LYS A 764 " pdb=" N CYS A 765 " pdb=" CA CYS A 765 " ideal model delta harmonic sigma weight residual 180.00 121.51 58.49 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA LYS C 764 " pdb=" C LYS C 764 " pdb=" N CYS C 765 " pdb=" CA CYS C 765 " ideal model delta harmonic sigma weight residual 180.00 121.56 58.44 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 321 " pdb=" CB CYS B 321 " ideal model delta sinusoidal sigma weight residual -86.00 -7.29 -78.71 1 1.00e+01 1.00e-02 7.72e+01 ... (remaining 14059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.743: 3926 0.743 - 1.486: 0 1.486 - 2.229: 0 2.229 - 2.972: 0 2.972 - 3.715: 2 Chirality restraints: 3928 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 1.31 -3.71 2.00e-02 2.50e+03 3.45e+04 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 1.31 -3.71 2.00e-02 2.50e+03 3.44e+04 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 -2.54 0.14 2.00e-02 2.50e+03 4.88e+01 ... (remaining 3925 not shown) Planarity restraints: 4152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 813 " 0.023 2.00e-02 2.50e+03 1.64e-02 6.72e+00 pdb=" CG TRP C 813 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 813 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 813 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 813 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 813 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 813 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 813 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 813 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 813 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 813 " -0.022 2.00e-02 2.50e+03 1.62e-02 6.60e+00 pdb=" CG TRP A 813 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 813 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 813 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 813 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 813 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 813 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 813 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 813 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 813 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 567 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO C 568 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 568 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 568 " -0.033 5.00e-02 4.00e+02 ... (remaining 4149 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 831 2.68 - 3.24: 25441 3.24 - 3.79: 35411 3.79 - 4.35: 43273 4.35 - 4.90: 70471 Nonbonded interactions: 175427 Sorted by model distance: nonbonded pdb=" O ASP A 324 " pdb=" NE1 TRP A 336 " model vdw 2.127 2.520 nonbonded pdb=" O ASP C 324 " pdb=" NE1 TRP C 336 " model vdw 2.127 2.520 nonbonded pdb=" OD1 ASP D 77 " pdb=" N SER D 80 " model vdw 2.152 2.520 nonbonded pdb=" OD1 ASP B 77 " pdb=" N SER B 80 " model vdw 2.153 2.520 nonbonded pdb=" OD1 ASP D 101 " pdb=" N ASP D 102 " model vdw 2.188 2.520 ... (remaining 175422 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' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 14940 2.51 5 N 3856 2.21 5 O 4440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.880 Check model and map are aligned: 0.370 Convert atoms to be neutral: 0.210 Process input model: 61.780 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.007 0.065 23850 Z= 0.441 Angle : 0.835 13.271 32582 Z= 0.469 Chirality : 0.097 3.715 3928 Planarity : 0.005 0.061 4140 Dihedral : 13.764 87.292 8068 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.47 % Favored : 85.09 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % 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: -4.55 (0.12), residues: 3158 helix: -1.66 (0.12), residues: 1276 sheet: -4.13 (0.21), residues: 372 loop : -4.04 (0.12), residues: 1510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 253 time to evaluate : 2.582 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 269 average time/residue: 0.2885 time to fit residues: 129.6994 Evaluate side-chains 202 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2026 time to fit residues: 7.8020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 286 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 86 GLN A 134 HIS A 147 GLN A 217 GLN A 311 GLN A 314 HIS A 392 HIS A 426 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS C 86 GLN C 134 HIS C 147 GLN C 217 GLN C 311 GLN C 314 HIS C 392 HIS C 426 GLN ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 23850 Z= 0.400 Angle : 0.789 12.154 32582 Z= 0.416 Chirality : 0.048 0.255 3928 Planarity : 0.005 0.056 4140 Dihedral : 6.447 60.165 3430 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.29 % Favored : 87.40 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % 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: -3.24 (0.14), residues: 3158 helix: -0.16 (0.14), residues: 1272 sheet: -3.68 (0.22), residues: 392 loop : -3.62 (0.14), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 196 time to evaluate : 2.696 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 46 residues processed: 258 average time/residue: 0.2840 time to fit residues: 124.4172 Evaluate side-chains 232 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 2.716 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2090 time to fit residues: 21.6431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 287 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 230 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 23850 Z= 0.187 Angle : 0.678 11.450 32582 Z= 0.353 Chirality : 0.044 0.249 3928 Planarity : 0.004 0.057 4140 Dihedral : 5.898 60.580 3430 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.34 % Favored : 90.41 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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: -2.29 (0.15), residues: 3158 helix: 0.65 (0.14), residues: 1286 sheet: -3.17 (0.23), residues: 454 loop : -3.10 (0.15), residues: 1418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 235 time to evaluate : 2.957 Fit side-chains outliers start: 43 outliers final: 9 residues processed: 266 average time/residue: 0.2796 time to fit residues: 126.7223 Evaluate side-chains 206 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 197 time to evaluate : 2.685 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1990 time to fit residues: 6.9779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 149 optimal weight: 0.0670 chunk 31 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 193 optimal weight: 0.1980 chunk 288 optimal weight: 0.8980 chunk 305 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 273 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 23850 Z= 0.168 Angle : 0.649 11.635 32582 Z= 0.335 Chirality : 0.043 0.247 3928 Planarity : 0.004 0.052 4140 Dihedral : 5.552 61.398 3430 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.06 % Favored : 90.75 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.84 (0.15), residues: 3158 helix: 1.01 (0.14), residues: 1294 sheet: -2.88 (0.23), residues: 470 loop : -2.87 (0.16), residues: 1394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 2.749 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 258 average time/residue: 0.2810 time to fit residues: 123.8059 Evaluate side-chains 224 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 2.597 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2139 time to fit residues: 11.3152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 260 optimal weight: 0.0270 chunk 211 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 23850 Z= 0.338 Angle : 0.711 11.778 32582 Z= 0.368 Chirality : 0.045 0.301 3928 Planarity : 0.005 0.051 4140 Dihedral : 5.680 63.330 3430 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.39 % Favored : 89.36 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.71 (0.15), residues: 3158 helix: 1.18 (0.14), residues: 1280 sheet: -2.75 (0.24), residues: 452 loop : -2.85 (0.16), residues: 1426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 206 time to evaluate : 2.522 Fit side-chains outliers start: 55 outliers final: 22 residues processed: 252 average time/residue: 0.2847 time to fit residues: 122.8870 Evaluate side-chains 217 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 2.598 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2296 time to fit residues: 13.1312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 305 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 23850 Z= 0.233 Angle : 0.697 13.955 32582 Z= 0.356 Chirality : 0.044 0.345 3928 Planarity : 0.004 0.050 4140 Dihedral : 5.557 63.539 3430 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.78 % Favored : 90.03 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.62 (0.15), residues: 3158 helix: 1.20 (0.14), residues: 1304 sheet: -2.65 (0.25), residues: 430 loop : -2.86 (0.16), residues: 1424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 2.829 Fit side-chains outliers start: 33 outliers final: 9 residues processed: 229 average time/residue: 0.2962 time to fit residues: 116.6339 Evaluate side-chains 207 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 2.720 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2054 time to fit residues: 7.0548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 chunk 174 optimal weight: 0.0270 chunk 223 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 23850 Z= 0.281 Angle : 0.718 11.581 32582 Z= 0.366 Chirality : 0.045 0.317 3928 Planarity : 0.005 0.049 4140 Dihedral : 5.576 63.911 3430 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.54 % Favored : 89.27 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.62 (0.15), residues: 3158 helix: 1.25 (0.14), residues: 1310 sheet: -2.71 (0.24), residues: 438 loop : -2.91 (0.16), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 2.732 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 216 average time/residue: 0.3003 time to fit residues: 109.2748 Evaluate side-chains 204 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 2.876 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2283 time to fit residues: 8.4305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 chunk 277 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 23850 Z= 0.400 Angle : 0.788 12.170 32582 Z= 0.401 Chirality : 0.047 0.293 3928 Planarity : 0.005 0.047 4140 Dihedral : 5.781 64.322 3430 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.49 % Favored : 88.32 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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: -1.75 (0.15), residues: 3158 helix: 1.16 (0.14), residues: 1308 sheet: -2.75 (0.24), residues: 428 loop : -3.00 (0.15), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 2.966 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 222 average time/residue: 0.2999 time to fit residues: 112.1888 Evaluate side-chains 210 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 2.661 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2817 time to fit residues: 11.1734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 23850 Z= 0.332 Angle : 0.760 12.908 32582 Z= 0.386 Chirality : 0.046 0.278 3928 Planarity : 0.005 0.047 4140 Dihedral : 5.785 66.673 3430 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.96 % Favored : 88.85 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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: -1.71 (0.15), residues: 3158 helix: 1.20 (0.14), residues: 1306 sheet: -2.86 (0.24), residues: 430 loop : -2.92 (0.15), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 2.941 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 215 average time/residue: 0.3059 time to fit residues: 112.7497 Evaluate side-chains 205 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 196 time to evaluate : 2.762 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2397 time to fit residues: 7.5190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 289 optimal weight: 40.0000 chunk 250 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 199 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 23850 Z= 0.266 Angle : 0.738 13.217 32582 Z= 0.371 Chirality : 0.046 0.333 3928 Planarity : 0.005 0.047 4140 Dihedral : 5.699 65.955 3430 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.54 % Favored : 89.30 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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: -1.54 (0.15), residues: 3158 helix: 1.34 (0.14), residues: 1306 sheet: -2.78 (0.25), residues: 400 loop : -2.86 (0.15), residues: 1452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 2.794 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 211 average time/residue: 0.2953 time to fit residues: 106.3251 Evaluate side-chains 205 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 201 time to evaluate : 2.703 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2570 time to fit residues: 5.5071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 231 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 251 optimal weight: 0.0030 chunk 105 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 31 optimal weight: 0.0040 chunk 46 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.094174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.070056 restraints weight = 83529.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072104 restraints weight = 42562.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.073430 restraints weight = 28228.166| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 23850 Z= 0.185 Angle : 0.706 13.248 32582 Z= 0.351 Chirality : 0.045 0.323 3928 Planarity : 0.004 0.049 4140 Dihedral : 5.456 65.597 3430 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.50 % Favored : 90.31 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.37 (0.16), residues: 3158 helix: 1.48 (0.15), residues: 1298 sheet: -2.76 (0.23), residues: 462 loop : -2.67 (0.16), residues: 1398 =============================================================================== Job complete usr+sys time: 3622.24 seconds wall clock time: 67 minutes 18.97 seconds (4038.97 seconds total)