Starting phenix.real_space_refine on Mon Dec 11 18:57:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/12_2023/8wpu_37724_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/12_2023/8wpu_37724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/12_2023/8wpu_37724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/12_2023/8wpu_37724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/12_2023/8wpu_37724_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/12_2023/8wpu_37724_updated.pdb" } resolution = 3.1 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= 0.007 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 101 5.16 5 C 12107 2.51 5 N 3124 2.21 5 O 3450 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G ASP 85": "OD1" <-> "OD2" Residue "G ASP 124": "OD1" <-> "OD2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 18794 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6178 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 31, 'TRANS': 776} Chain breaks: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 18, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 172 Chain: "A" Number of atoms: 6169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6169 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 31, 'TRANS': 771} Chain breaks: 3 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 139 Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1619 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 3, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 127 Chain: "C" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2523 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 356 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1643 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 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: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 132 Unusual residues: {' CA': 2, 'CLR': 1, 'NAG': 4, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1106 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 118 Unusual residues: {' CA': 2, 'NAG': 5, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1107 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.14, per 1000 atoms: 0.54 Number of scatterers: 18794 At special positions: 0 Unit cell: (147.66, 120.91, 245.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 101 16.00 P 2 15.00 F 6 9.00 O 3450 8.00 N 3124 7.00 C 12107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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 F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1102 " - " ASN A 261 " " NAG A1103 " - " ASN A 287 " " NAG A1104 " - " ASN A 488 " " NAG A1105 " - " ASN A 468 " " NAG A1106 " - " ASN A 594 " " NAG B1101 " - " ASN B 261 " " NAG B1102 " - " ASN B 287 " " NAG B1103 " - " ASN B 468 " " NAG B1104 " - " ASN B 594 " " NAG F 1 " - " ASN B 541 " " NAG H 1 " - " ASN A 541 " Time building additional restraints: 7.78 Conformation dependent library (CDL) restraints added in 3.5 seconds 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 26 sheets defined 34.0% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.655A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.504A pdb=" N SER B 175 " --> pdb=" O ARG B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 192 through 203 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 613 through 636 Processing helix chain 'B' and resid 644 through 646 No H-bonds generated for 'chain 'B' and resid 644 through 646' Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.673A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU B 666 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 677 No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 680 through 698 removed outlier: 3.531A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 745 removed outlier: 3.583A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.633A pdb=" N LYS B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 825 removed outlier: 4.236A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 837 through 860 removed outlier: 3.633A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 867 removed outlier: 4.469A pdb=" N ARG B 866 " --> pdb=" O LYS B 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 147 through 157 removed outlier: 3.813A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 190 through 203 Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 273 through 285 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.788A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 611 through 636 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 648 through 667 removed outlier: 3.707A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 678 No H-bonds generated for 'chain 'A' and resid 675 through 678' Processing helix chain 'A' and resid 681 through 705 removed outlier: 3.524A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 702 " --> pdb=" O LYS A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 744 removed outlier: 4.088A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 796 removed outlier: 3.523A pdb=" N THR A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS A 796 " --> pdb=" O PHE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 801 No H-bonds generated for 'chain 'A' and resid 799 through 801' Processing helix chain 'A' and resid 804 through 820 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 831 through 861 removed outlier: 3.605A pdb=" N SER A 834 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 836 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER A 845 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 846 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A 853 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE A 854 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN A 855 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 32 removed outlier: 3.767A pdb=" N GLU G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'G' and resid 46 through 49 No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 147 through 153 removed outlier: 4.344A pdb=" N GLU G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 184 through 203 removed outlier: 3.983A pdb=" N PHE G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG G 194 " --> pdb=" O LYS G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 242 removed outlier: 3.798A pdb=" N ASP G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 5 No H-bonds generated for 'chain 'C' and resid 2 through 5' Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.768A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'D' and resid 12 through 15 No H-bonds generated for 'chain 'D' and resid 12 through 15' Processing helix chain 'D' and resid 19 through 22 No H-bonds generated for 'chain 'D' and resid 19 through 22' Processing helix chain 'D' and resid 30 through 43 removed outlier: 4.670A pdb=" N ALA D 35 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N MET D 38 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 43 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.518A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.254A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 319 through 322 removed outlier: 3.693A pdb=" N GLY B 509 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 550 through 554 Processing sheet with id= E, first strand: chain 'B' and resid 602 through 604 Processing sheet with id= F, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.184A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 37 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 292 through 295 removed outlier: 7.184A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N CYS A 236 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR A 211 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP A 238 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 12.483A pdb=" N ALA A 213 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N SER A 240 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.356A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= J, first strand: chain 'A' and resid 550 through 554 Processing sheet with id= K, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= L, first strand: chain 'A' and resid 749 through 753 Processing sheet with id= M, first strand: chain 'G' and resid 138 through 144 removed outlier: 4.119A pdb=" N ALA G 105 " --> pdb=" O ARG G 35 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.694A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.627A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.522A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 198 through 202 removed outlier: 3.667A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.526A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.564A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.666A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.528A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 92 through 94 Processing sheet with id= W, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.579A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 142 through 148 removed outlier: 3.875A pdb=" N VAL E 143 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE E 145 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 163 through 165 Processing sheet with id= Z, first strand: chain 'E' and resid 35 through 39 removed outlier: 3.633A pdb=" N TRP E 36 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z 646 hydrogen bonds defined for protein. 1785 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: 6.79 Time building geometry restraints manager: 8.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3169 1.32 - 1.45: 5376 1.45 - 1.57: 10568 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 19238 Sorted by residual: bond pdb=" N ARG B 69 " pdb=" CA ARG B 69 " ideal model delta sigma weight residual 1.459 1.383 0.076 1.17e-02 7.31e+03 4.17e+01 bond pdb=" CA LYS A 805 " pdb=" C LYS A 805 " ideal model delta sigma weight residual 1.524 1.446 0.078 1.26e-02 6.30e+03 3.79e+01 bond pdb=" CA ARG B 69 " pdb=" C ARG B 69 " ideal model delta sigma weight residual 1.524 1.459 0.066 1.24e-02 6.50e+03 2.79e+01 bond pdb=" C ASP C 246 " pdb=" N ASP C 247 " ideal model delta sigma weight residual 1.334 1.275 0.059 1.24e-02 6.50e+03 2.27e+01 bond pdb=" CA ARG A 795 " pdb=" C ARG A 795 " ideal model delta sigma weight residual 1.523 1.462 0.060 1.37e-02 5.33e+03 1.94e+01 ... (remaining 19233 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.85: 320 105.85 - 112.89: 10337 112.89 - 119.92: 6297 119.92 - 126.96: 9031 126.96 - 134.00: 224 Bond angle restraints: 26209 Sorted by residual: angle pdb=" N ARG B 69 " pdb=" CA ARG B 69 " pdb=" C ARG B 69 " ideal model delta sigma weight residual 110.97 102.81 8.16 1.09e+00 8.42e-01 5.61e+01 angle pdb=" CA PRO B 89 " pdb=" N PRO B 89 " pdb=" CD PRO B 89 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 angle pdb=" O ILE B 599 " pdb=" C ILE B 599 " pdb=" N ALA B 600 " ideal model delta sigma weight residual 122.97 118.79 4.18 1.07e+00 8.73e-01 1.53e+01 angle pdb=" N ILE A 409 " pdb=" CA ILE A 409 " pdb=" C ILE A 409 " ideal model delta sigma weight residual 113.71 110.13 3.58 9.50e-01 1.11e+00 1.42e+01 angle pdb=" C ARG A 795 " pdb=" CA ARG A 795 " pdb=" CB ARG A 795 " ideal model delta sigma weight residual 110.38 102.80 7.58 2.04e+00 2.40e-01 1.38e+01 ... (remaining 26204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.77: 10920 31.77 - 63.53: 475 63.53 - 95.30: 29 95.30 - 127.06: 7 127.06 - 158.83: 2 Dihedral angle restraints: 11433 sinusoidal: 4313 harmonic: 7120 Sorted by residual: dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 -178.87 -88.13 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual 93.00 159.96 -66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS B 546 " pdb=" SG CYS B 546 " pdb=" SG CYS B 565 " pdb=" CB CYS B 565 " ideal model delta sinusoidal sigma weight residual -86.00 -139.29 53.29 1 1.00e+01 1.00e-02 3.86e+01 ... (remaining 11430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2557 0.058 - 0.115: 425 0.115 - 0.173: 39 0.173 - 0.231: 1 0.231 - 0.288: 3 Chirality restraints: 3025 Sorted by residual: chirality pdb=" CB ILE B 741 " pdb=" CA ILE B 741 " pdb=" CG1 ILE B 741 " pdb=" CG2 ILE B 741 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 541 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA YP4 A1110 " pdb=" N YP4 A1110 " pdb=" CB YP4 A1110 " pdb=" C1 YP4 A1110 " both_signs ideal model delta sigma weight residual False -2.41 -2.65 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3022 not shown) Planarity restraints: 3322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 88 " 0.088 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO B 89 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO B 89 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 89 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 804 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.87e+00 pdb=" C ALA A 804 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 804 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 805 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 245 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C SER C 245 " 0.038 2.00e-02 2.50e+03 pdb=" O SER C 245 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP C 246 " -0.013 2.00e-02 2.50e+03 ... (remaining 3319 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 684 2.71 - 3.26: 19176 3.26 - 3.81: 31423 3.81 - 4.35: 38476 4.35 - 4.90: 65527 Nonbonded interactions: 155286 Sorted by model distance: nonbonded pdb=" O ASP A 570 " pdb=" OG SER A 591 " model vdw 2.163 2.440 nonbonded pdb=" OH TYR G 212 " pdb=" OD1 ASP G 233 " model vdw 2.201 2.440 nonbonded pdb=" O ALA B 548 " pdb=" OG SER B 574 " model vdw 2.204 2.440 nonbonded pdb=" O4 NAG A1106 " pdb=" O7 NAG A1106 " model vdw 2.212 2.440 nonbonded pdb=" O SER A 794 " pdb=" OG SER A 794 " model vdw 2.225 2.440 ... (remaining 155281 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' and (resid 20 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 or (resid 61 and (name N or n \ ame CA or name C or name O or name CB )) or resid 62 through 123 or (resid 124 t \ hrough 125 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 230 or (resid 231 and (name N or name CA or name C or n \ ame O or name CB )) or resid 232 through 252 or (resid 253 and (name N or name C \ A or name C or name O or name CB )) or resid 254 through 269 or (resid 270 and ( \ name N or name CA or name C or name O or name CB )) or resid 271 through 296 or \ (resid 297 through 298 and (name N or name CA or name C or name O or name CB )) \ or resid 299 through 393 or (resid 394 and (name N or name CA or name C or name \ O or name CB )) or resid 395 through 432 or (resid 433 and (name N or name CA or \ name C or name O or name CB )) or resid 434 through 450 or (resid 451 and (name \ N or name CA or name C or name O or name CB )) or resid 452 through 454 or (res \ id 455 through 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 461 or (resid 462 and (name N or name CA or name C or name O or \ name CB )) or resid 463 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 518 or (resid 519 and (name N o \ r name CA or name C or name O or name CB )) or resid 520 through 525 or (resid 5 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 527 through \ 543 or (resid 544 and (name N or name CA or name C or name O or name CB )) or r \ esid 545 through 551 or (resid 552 and (name N or name CA or name C or name O or \ name CB )) or resid 553 through 575 or (resid 576 and (name N or name CA or nam \ e C or name O or name CB )) or resid 577 or (resid 578 through 579 and (name N o \ r name CA or name C or name O or name CB )) or resid 580 through 583 or (resid 5 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 585 through \ 586 or (resid 587 through 588 and (name N or name CA or name C or name O or nam \ e CB )) or resid 589 through 591 or (resid 592 through 593 and (name N or name C \ A or name C or name O or name CB )) or resid 594 through 635 or (resid 636 throu \ gh 637 and (name N or name CA or name C or name O or name CB )) or resid 638 thr \ ough 641 or (resid 642 and (name N or name CA or name C or name O or name CB )) \ or resid 643 through 664 or (resid 665 and (name N or name CA or name C or name \ O or name CB )) or resid 666 through 673 or (resid 674 and (name N or name CA or \ name C or name O or name CB )) or resid 675 through 704 or (resid 705 and (name \ N or name CA or name C or name O or name CB )) or resid 719 through 723 or (res \ id 724 and (name N or name CA or name C or name O or name CB )) or resid 725 or \ (resid 726 and (name N or name CA or name C or name O or name CB )) or resid 727 \ through 770 or (resid 771 through 772 and (name N or name CA or name C or name \ O or name CB )) or resid 773 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 through 802 or (resid 803 through 8 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 805 through \ 809 or (resid 810 and (name N or name CA or name C or name O or name CB )) or r \ esid 811 through 862 or (resid 863 and (name N or name CA or name C or name O or \ name CB )) or resid 864 through 865 or resid 1102 through 1105 or resid 1107 th \ rough 1108)) selection = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 131 or (resid 132 thr \ ough 135 and (name N or name CA or name C or name O or name CB )) or resid 136 t \ hrough 322 or (resid 323 through 324 and (name N or name CA or name C or name O \ or name CB )) or resid 325 through 348 or (resid 349 and (name N or name CA or n \ ame C or name O or name CB )) or resid 350 through 360 or (resid 361 and (name N \ or name CA or name C or name O or name CB )) or (resid 392 and (name N or name \ CA or name C or name O or name CB )) or resid 393 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 404 or \ (resid 405 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 6 through 445 or (resid 446 and (name N or name CA or name C or name O or name C \ B )) or resid 447 through 452 or (resid 453 through 457 and (name N or name CA o \ r name C or name O or name CB )) or resid 458 through 475 or (resid 476 and (nam \ e N or name CA or name C or name O or name CB )) or resid 477 through 480 or (re \ sid 481 and (name N or name CA or name C or name O or name CB )) or resid 482 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 535 or (resid 536 and (name N or name CA o \ r name C or name O or name CB )) or resid 537 through 603 or (resid 604 and (nam \ e N or name CA or name C or name O or name CB )) or resid 605 through 609 or (re \ sid 610 and (name N or name CA or name C or name O or name CB )) or resid 611 th \ rough 621 or (resid 622 and (name N or name CA or name C or name O or name CB )) \ or resid 623 through 624 or (resid 625 and (name N or name CA or name C or name \ O or name CB )) or resid 626 through 660 or (resid 661 and (name N or name CA o \ r name C or name O or name CB )) or resid 662 through 670 or (resid 671 and (nam \ e N or name CA or name C or name O or name CB )) or resid 672 through 705 or (re \ sid 719 and (name N or name CA or name C or name O or name CB )) or resid 720 th \ rough 729 or (resid 730 and (name N or name CA or name C or name O or name CB )) \ or resid 731 through 732 or (resid 733 through 734 and (name N or name CA or na \ me C or name O or name CB )) or resid 735 through 736 or (resid 737 and (name N \ or name CA or name C or name O or name CB )) or resid 738 or (resid 739 and (nam \ e N or name CA or name C or name O or name CB )) or resid 740 through 758 or (re \ sid 759 and (name N or name CA or name C or name O or name CB )) or resid 760 th \ rough 792 or (resid 793 through 794 and (name N or name CA or name C or name O o \ r name CB )) or resid 795 through 830 or (resid 831 and (name N or name CA or na \ me C or name O or name CB )) or resid 832 through 865 or resid 1101 through 1104 \ or resid 1106 through 1107)) } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.110 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 53.290 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.004 0.080 19238 Z= 0.272 Angle : 0.588 9.205 26209 Z= 0.318 Chirality : 0.043 0.288 3025 Planarity : 0.004 0.130 3311 Dihedral : 16.874 158.829 6776 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 28.01 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2423 helix: 0.72 (0.18), residues: 830 sheet: -1.22 (0.26), residues: 412 loop : -0.96 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 608 HIS 0.006 0.001 HIS C 142 PHE 0.030 0.001 PHE G 192 TYR 0.021 0.001 TYR E 223 ARG 0.008 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3206 time to fit residues: 120.7912 Evaluate side-chains 236 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 189 optimal weight: 2.9990 chunk 73 optimal weight: 0.0570 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN B 345 ASN A 735 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19238 Z= 0.187 Angle : 0.519 7.895 26209 Z= 0.272 Chirality : 0.042 0.197 3025 Planarity : 0.004 0.078 3311 Dihedral : 8.778 154.466 2979 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.49 % Allowed : 25.70 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2423 helix: 0.82 (0.18), residues: 825 sheet: -1.10 (0.26), residues: 422 loop : -0.95 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE B 806 TYR 0.020 0.001 TYR E 223 ARG 0.006 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 243 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 32 residues processed: 284 average time/residue: 0.3146 time to fit residues: 136.9435 Evaluate side-chains 263 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 2.098 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1856 time to fit residues: 13.9195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 237 optimal weight: 0.0870 chunk 196 optimal weight: 0.9990 chunk 218 optimal weight: 0.4980 chunk 75 optimal weight: 0.0070 chunk 176 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN B 72 GLN A 463 HIS ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19238 Z= 0.172 Angle : 0.498 9.017 26209 Z= 0.259 Chirality : 0.041 0.195 3025 Planarity : 0.004 0.056 3311 Dihedral : 7.836 151.392 2979 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.58 % Allowed : 26.40 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2423 helix: 0.85 (0.18), residues: 828 sheet: -1.08 (0.26), residues: 410 loop : -0.95 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE A 605 TYR 0.021 0.001 TYR E 223 ARG 0.005 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 15 residues processed: 283 average time/residue: 0.3152 time to fit residues: 137.1364 Evaluate side-chains 250 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 235 time to evaluate : 2.291 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2220 time to fit residues: 8.5673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 114 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 595 HIS ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 19238 Z= 0.418 Angle : 0.593 10.306 26209 Z= 0.311 Chirality : 0.045 0.241 3025 Planarity : 0.004 0.061 3311 Dihedral : 7.685 155.302 2979 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.14 % Allowed : 25.65 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2423 helix: 0.67 (0.18), residues: 823 sheet: -1.37 (0.25), residues: 451 loop : -1.05 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 530 HIS 0.008 0.001 HIS E 35 PHE 0.021 0.002 PHE A 789 TYR 0.025 0.002 TYR E 223 ARG 0.004 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 242 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 39 residues processed: 296 average time/residue: 0.3157 time to fit residues: 145.6917 Evaluate side-chains 269 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 2.136 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.1727 time to fit residues: 15.5727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN A 466 HIS ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 19238 Z= 0.507 Angle : 0.655 11.169 26209 Z= 0.345 Chirality : 0.048 0.253 3025 Planarity : 0.005 0.082 3311 Dihedral : 7.517 143.728 2979 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.92 % Allowed : 26.02 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2423 helix: 0.29 (0.18), residues: 836 sheet: -1.51 (0.24), residues: 456 loop : -1.19 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 530 HIS 0.008 0.001 HIS E 35 PHE 0.025 0.002 PHE A 605 TYR 0.032 0.002 TYR E 223 ARG 0.007 0.001 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 234 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 34 residues processed: 294 average time/residue: 0.3105 time to fit residues: 142.0470 Evaluate side-chains 262 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 228 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1766 time to fit residues: 14.1129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 0.5980 chunk 210 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN B 312 HIS B 476 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN G 214 HIS ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19238 Z= 0.215 Angle : 0.526 8.016 26209 Z= 0.277 Chirality : 0.042 0.207 3025 Planarity : 0.004 0.045 3311 Dihedral : 6.630 121.793 2979 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.63 % Allowed : 26.61 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2423 helix: 0.67 (0.18), residues: 822 sheet: -1.43 (0.24), residues: 454 loop : -1.06 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 82 HIS 0.006 0.001 HIS C 142 PHE 0.028 0.001 PHE G 192 TYR 0.030 0.001 TYR E 223 ARG 0.006 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 248 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 21 residues processed: 280 average time/residue: 0.3122 time to fit residues: 133.2392 Evaluate side-chains 259 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 238 time to evaluate : 1.973 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1709 time to fit residues: 9.5749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 197 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19238 Z= 0.320 Angle : 0.568 8.888 26209 Z= 0.297 Chirality : 0.044 0.220 3025 Planarity : 0.004 0.047 3311 Dihedral : 6.546 121.186 2979 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.45 % Allowed : 27.80 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2423 helix: 0.63 (0.18), residues: 823 sheet: -1.43 (0.24), residues: 455 loop : -1.09 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 530 HIS 0.007 0.001 HIS E 35 PHE 0.026 0.002 PHE G 192 TYR 0.027 0.002 TYR E 223 ARG 0.008 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 243 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 259 average time/residue: 0.3214 time to fit residues: 128.2786 Evaluate side-chains 248 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 239 time to evaluate : 2.065 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1776 time to fit residues: 5.8297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19238 Z= 0.261 Angle : 0.545 8.602 26209 Z= 0.285 Chirality : 0.043 0.206 3025 Planarity : 0.004 0.046 3311 Dihedral : 6.324 112.564 2979 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.34 % Allowed : 28.01 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2423 helix: 0.68 (0.18), residues: 822 sheet: -1.27 (0.25), residues: 442 loop : -1.09 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.028 0.002 PHE G 192 TYR 0.027 0.001 TYR E 223 ARG 0.008 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 239 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 253 average time/residue: 0.3098 time to fit residues: 121.2024 Evaluate side-chains 246 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 232 time to evaluate : 2.275 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1786 time to fit residues: 7.4931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 217 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 196 optimal weight: 0.5980 chunk 205 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19238 Z= 0.236 Angle : 0.535 9.855 26209 Z= 0.280 Chirality : 0.042 0.198 3025 Planarity : 0.004 0.045 3311 Dihedral : 6.063 103.923 2979 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.02 % Allowed : 28.49 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2423 helix: 0.70 (0.18), residues: 821 sheet: -1.21 (0.25), residues: 436 loop : -1.05 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.029 0.001 PHE G 192 TYR 0.023 0.001 TYR E 223 ARG 0.007 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 246 average time/residue: 0.3224 time to fit residues: 122.2319 Evaluate side-chains 246 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 237 time to evaluate : 2.144 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1859 time to fit residues: 5.9210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 241 optimal weight: 0.6980 chunk 221 optimal weight: 0.0040 chunk 191 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 117 optimal weight: 0.0870 chunk 152 optimal weight: 0.6980 overall best weight: 0.3770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19238 Z= 0.164 Angle : 0.511 9.415 26209 Z= 0.266 Chirality : 0.041 0.212 3025 Planarity : 0.004 0.044 3311 Dihedral : 5.674 93.109 2979 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.22 % Allowed : 29.14 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2423 helix: 0.84 (0.18), residues: 819 sheet: -1.15 (0.25), residues: 429 loop : -0.97 (0.19), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.028 0.001 PHE G 192 TYR 0.017 0.001 TYR E 223 ARG 0.007 0.000 ARG A 752 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 249 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 251 average time/residue: 0.3272 time to fit residues: 127.2713 Evaluate side-chains 237 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 2.184 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1735 time to fit residues: 3.8696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 177 optimal weight: 0.0010 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.0020 chunk 192 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.095235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.080733 restraints weight = 45778.607| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.19 r_work: 0.3276 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19238 Z= 0.252 Angle : 0.534 8.320 26209 Z= 0.280 Chirality : 0.043 0.215 3025 Planarity : 0.004 0.044 3311 Dihedral : 5.698 95.498 2979 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.43 % Allowed : 29.95 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2423 helix: 0.77 (0.18), residues: 821 sheet: -1.17 (0.25), residues: 431 loop : -0.99 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 530 HIS 0.006 0.001 HIS E 35 PHE 0.030 0.001 PHE G 192 TYR 0.019 0.001 TYR E 223 ARG 0.008 0.000 ARG A 752 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4666.58 seconds wall clock time: 85 minutes 0.71 seconds (5100.71 seconds total)