Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 17:59:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/04_2023/7rlu_24547_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/04_2023/7rlu_24547.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/04_2023/7rlu_24547_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/04_2023/7rlu_24547_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/04_2023/7rlu_24547_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/04_2023/7rlu_24547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/04_2023/7rlu_24547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/04_2023/7rlu_24547_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/04_2023/7rlu_24547_updated.pdb" } resolution = 2.9 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 11508 2.51 5 N 3088 2.21 5 O 3484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A ARG 894": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "B GLU 717": "OE1" <-> "OE2" Residue "B PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 894": "NH1" <-> "NH2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D ARG 894": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 894": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18188 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4492 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 560} Chain breaks: 1 Chain: "B" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4492 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 560} Chain breaks: 1 Chain: "D" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4492 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 560} Chain breaks: 1 Chain: "C" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4492 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 560} Chain breaks: 1 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'NAP': 1, 'PNS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'NAP': 1, 'PNS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 10.29, per 1000 atoms: 0.57 Number of scatterers: 18188 At special positions: 0 Unit cell: (99.56, 108.68, 117.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 12 15.00 O 3484 8.00 N 3088 7.00 C 11508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.47 Conformation dependent library (CDL) restraints added in 3.1 seconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 24 sheets defined 43.0% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.755A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.809A pdb=" N GLY A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 351' Processing helix chain 'A' and resid 354 through 367 removed outlier: 3.976A pdb=" N VAL A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 458 through 473 Processing helix chain 'A' and resid 476 through 479 No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.743A pdb=" N LYS A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.981A pdb=" N SER A 526 " --> pdb=" O HIS A 522 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 590 removed outlier: 3.813A pdb=" N LEU A 580 " --> pdb=" O PRO A 576 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA A 586 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.524A pdb=" N LEU A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 removed outlier: 4.074A pdb=" N GLN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.807A pdb=" N HIS A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 666 " --> pdb=" O CYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 699 removed outlier: 3.701A pdb=" N VAL A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 5.489A pdb=" N ASN A 721 " --> pdb=" O SER A 718 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 722 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 724 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 725 " --> pdb=" O GLN A 722 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 728 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 729 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 732 " --> pdb=" O GLU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 768 removed outlier: 3.792A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 802 No H-bonds generated for 'chain 'A' and resid 799 through 802' Processing helix chain 'A' and resid 820 through 828 Processing helix chain 'A' and resid 843 through 852 Processing helix chain 'A' and resid 887 through 892 removed outlier: 4.112A pdb=" N GLU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 892' Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.668A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.805A pdb=" N GLY B 351 " --> pdb=" O PHE B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 351' Processing helix chain 'B' and resid 354 through 367 removed outlier: 4.005A pdb=" N VAL B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 384 through 395 Processing helix chain 'B' and resid 458 through 473 Processing helix chain 'B' and resid 476 through 479 No H-bonds generated for 'chain 'B' and resid 476 through 479' Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.737A pdb=" N LYS B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 536 removed outlier: 3.984A pdb=" N SER B 526 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP B 536 " --> pdb=" O TYR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 590 removed outlier: 3.788A pdb=" N LEU B 580 " --> pdb=" O PRO B 576 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 583 " --> pdb=" O MET B 579 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 586 " --> pdb=" O TRP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 removed outlier: 3.524A pdb=" N LEU B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 639 removed outlier: 4.085A pdb=" N GLN B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 638 " --> pdb=" O GLY B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 removed outlier: 3.558A pdb=" N HIS B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 658 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 666 " --> pdb=" O CYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 699 removed outlier: 3.695A pdb=" N VAL B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 733 removed outlier: 5.535A pdb=" N ASN B 721 " --> pdb=" O SER B 718 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 722 " --> pdb=" O ILE B 719 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 724 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 725 " --> pdb=" O GLN B 722 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 728 " --> pdb=" O GLN B 725 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 729 " --> pdb=" O LYS B 726 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 732 " --> pdb=" O GLU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 768 removed outlier: 3.794A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 768 " --> pdb=" O ARG B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 802 No H-bonds generated for 'chain 'B' and resid 799 through 802' Processing helix chain 'B' and resid 820 through 828 Processing helix chain 'B' and resid 843 through 852 Processing helix chain 'B' and resid 887 through 892 removed outlier: 4.110A pdb=" N GLU B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR B 892 " --> pdb=" O ALA B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 887 through 892' Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.758A pdb=" N ALA D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 removed outlier: 3.818A pdb=" N GLY D 351 " --> pdb=" O PHE D 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 347 through 351' Processing helix chain 'D' and resid 354 through 367 removed outlier: 3.977A pdb=" N VAL D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 380 removed outlier: 3.554A pdb=" N TYR D 379 " --> pdb=" O ASN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 395 Processing helix chain 'D' and resid 458 through 473 Processing helix chain 'D' and resid 476 through 479 No H-bonds generated for 'chain 'D' and resid 476 through 479' Processing helix chain 'D' and resid 482 through 498 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.749A pdb=" N LYS D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 removed outlier: 3.981A pdb=" N SER D 526 " --> pdb=" O HIS D 522 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY D 535 " --> pdb=" O ARG D 531 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP D 536 " --> pdb=" O TYR D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 590 removed outlier: 3.789A pdb=" N LEU D 580 " --> pdb=" O PRO D 576 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 583 " --> pdb=" O MET D 579 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D 586 " --> pdb=" O TRP D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 616 removed outlier: 3.525A pdb=" N LEU D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 614 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS D 615 " --> pdb=" O GLU D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 639 removed outlier: 4.084A pdb=" N GLN D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 638 " --> pdb=" O GLY D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 666 removed outlier: 3.550A pdb=" N HIS D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN D 666 " --> pdb=" O CYS D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 699 removed outlier: 3.703A pdb=" N VAL D 699 " --> pdb=" O GLY D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 733 removed outlier: 5.460A pdb=" N ASN D 721 " --> pdb=" O SER D 718 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN D 722 " --> pdb=" O ILE D 719 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 724 " --> pdb=" O ASN D 721 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN D 725 " --> pdb=" O GLN D 722 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 728 " --> pdb=" O GLN D 725 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 729 " --> pdb=" O LYS D 726 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 732 " --> pdb=" O GLU D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 768 removed outlier: 3.796A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU D 768 " --> pdb=" O ARG D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 802 No H-bonds generated for 'chain 'D' and resid 799 through 802' Processing helix chain 'D' and resid 820 through 828 Processing helix chain 'D' and resid 843 through 852 Processing helix chain 'D' and resid 887 through 892 removed outlier: 4.042A pdb=" N GLU D 891 " --> pdb=" O ALA D 887 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR D 892 " --> pdb=" O ALA D 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 887 through 892' Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.752A pdb=" N ALA C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.812A pdb=" N GLY C 351 " --> pdb=" O PHE C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 347 through 351' Processing helix chain 'C' and resid 354 through 367 removed outlier: 3.974A pdb=" N VAL C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 384 through 395 Processing helix chain 'C' and resid 458 through 473 Processing helix chain 'C' and resid 476 through 479 No H-bonds generated for 'chain 'C' and resid 476 through 479' Processing helix chain 'C' and resid 482 through 498 Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 515 through 520 removed outlier: 3.745A pdb=" N LYS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 536 removed outlier: 3.978A pdb=" N SER C 526 " --> pdb=" O HIS C 522 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP C 536 " --> pdb=" O TYR C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 590 removed outlier: 3.811A pdb=" N LEU C 580 " --> pdb=" O PRO C 576 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 583 " --> pdb=" O MET C 579 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA C 586 " --> pdb=" O TRP C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 616 removed outlier: 3.525A pdb=" N LEU C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 615 " --> pdb=" O GLU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 removed outlier: 4.076A pdb=" N GLN C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 638 " --> pdb=" O GLY C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.567A pdb=" N HIS C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 658 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 666 " --> pdb=" O CYS C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 699 removed outlier: 3.708A pdb=" N VAL C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 733 removed outlier: 5.462A pdb=" N ASN C 721 " --> pdb=" O SER C 718 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN C 722 " --> pdb=" O ILE C 719 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 724 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN C 725 " --> pdb=" O GLN C 722 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 728 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 729 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 732 " --> pdb=" O GLU C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 768 removed outlier: 3.792A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU C 768 " --> pdb=" O ARG C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 802 No H-bonds generated for 'chain 'C' and resid 799 through 802' Processing helix chain 'C' and resid 820 through 828 Processing helix chain 'C' and resid 843 through 852 Processing helix chain 'C' and resid 887 through 890 No H-bonds generated for 'chain 'C' and resid 887 through 890' Processing sheet with id= A, first strand: chain 'A' and resid 408 through 412 removed outlier: 3.690A pdb=" N MET A 420 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.785A pdb=" N ALA A 543 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR A 557 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 623 through 625 removed outlier: 6.565A pdb=" N VAL A 594 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLY A 568 " --> pdb=" O ARG A 644 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A 646 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A 570 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 648 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS A 669 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N PHE A 648 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER A 671 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 857 through 860 removed outlier: 7.472A pdb=" N LEU A 680 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 713 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 682 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 715 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 809 through 811 removed outlier: 6.742A pdb=" N THR A 789 " --> pdb=" O MET A 810 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS A 774 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A 792 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A 772 " --> pdb=" O THR A 792 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 438 through 442 removed outlier: 4.320A pdb=" N CYS A 451 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 408 through 412 removed outlier: 3.693A pdb=" N MET B 420 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 543 through 545 removed outlier: 3.787A pdb=" N ALA B 543 " --> pdb=" O THR B 559 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 557 " --> pdb=" O ILE B 545 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 623 through 625 removed outlier: 6.566A pdb=" N VAL B 594 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLY B 568 " --> pdb=" O ARG B 644 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 646 " --> pdb=" O GLY B 568 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL B 570 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 648 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS B 669 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N PHE B 648 " --> pdb=" O LYS B 669 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER B 671 " --> pdb=" O PHE B 648 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 857 through 860 removed outlier: 7.473A pdb=" N LEU B 680 " --> pdb=" O GLY B 711 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 713 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 682 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 715 " --> pdb=" O ILE B 682 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 809 through 811 removed outlier: 6.742A pdb=" N THR B 789 " --> pdb=" O MET B 810 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS B 774 " --> pdb=" O VAL B 790 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 792 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU B 772 " --> pdb=" O THR B 792 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 438 through 442 removed outlier: 4.316A pdb=" N CYS B 451 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 408 through 412 removed outlier: 3.689A pdb=" N MET D 420 " --> pdb=" O VAL D 409 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 543 through 545 removed outlier: 3.787A pdb=" N ALA D 543 " --> pdb=" O THR D 559 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR D 557 " --> pdb=" O ILE D 545 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 623 through 625 removed outlier: 6.567A pdb=" N VAL D 594 " --> pdb=" O ASN D 624 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLY D 568 " --> pdb=" O ARG D 644 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE D 646 " --> pdb=" O GLY D 568 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL D 570 " --> pdb=" O ILE D 646 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE D 648 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS D 669 " --> pdb=" O ILE D 646 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N PHE D 648 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER D 671 " --> pdb=" O PHE D 648 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 857 through 860 removed outlier: 7.467A pdb=" N LEU D 680 " --> pdb=" O GLY D 711 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU D 713 " --> pdb=" O LEU D 680 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE D 682 " --> pdb=" O LEU D 713 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL D 715 " --> pdb=" O ILE D 682 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.737A pdb=" N THR D 789 " --> pdb=" O MET D 810 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS D 774 " --> pdb=" O VAL D 790 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR D 792 " --> pdb=" O LEU D 772 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU D 772 " --> pdb=" O THR D 792 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 438 through 442 removed outlier: 4.317A pdb=" N CYS D 451 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 408 through 412 removed outlier: 3.688A pdb=" N MET C 420 " --> pdb=" O VAL C 409 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 543 through 545 removed outlier: 3.784A pdb=" N ALA C 543 " --> pdb=" O THR C 559 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 557 " --> pdb=" O ILE C 545 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 623 through 625 removed outlier: 6.566A pdb=" N VAL C 594 " --> pdb=" O ASN C 624 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLY C 568 " --> pdb=" O ARG C 644 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 646 " --> pdb=" O GLY C 568 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C 570 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE C 648 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS C 669 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N PHE C 648 " --> pdb=" O LYS C 669 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER C 671 " --> pdb=" O PHE C 648 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 857 through 860 removed outlier: 7.468A pdb=" N LEU C 680 " --> pdb=" O GLY C 711 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU C 713 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 682 " --> pdb=" O LEU C 713 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 715 " --> pdb=" O ILE C 682 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 809 through 811 removed outlier: 6.735A pdb=" N THR C 789 " --> pdb=" O MET C 810 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS C 774 " --> pdb=" O VAL C 790 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR C 792 " --> pdb=" O LEU C 772 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU C 772 " --> pdb=" O THR C 792 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 438 through 442 removed outlier: 4.321A pdb=" N CYS C 451 " --> pdb=" O THR C 441 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 8.00 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: 5335 1.34 - 1.46: 2476 1.46 - 1.58: 10517 1.58 - 1.70: 16 1.70 - 1.82: 148 Bond restraints: 18492 Sorted by residual: bond pdb=" O3 NAP B1001 " pdb=" PA NAP B1001 " ideal model delta sigma weight residual 1.647 1.510 0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" O3 NAP D1001 " pdb=" PA NAP D1001 " ideal model delta sigma weight residual 1.647 1.510 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" O2B NAP A1001 " pdb=" P2B NAP A1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O2B NAP C1001 " pdb=" P2B NAP C1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" O2B NAP D1001 " pdb=" P2B NAP D1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 18487 not shown) Histogram of bond angle deviations from ideal: 100.15 - 107.43: 541 107.43 - 114.71: 10717 114.71 - 121.98: 8415 121.98 - 129.26: 5286 129.26 - 136.54: 85 Bond angle restraints: 25044 Sorted by residual: angle pdb=" O2A NAP D1001 " pdb=" PA NAP D1001 " pdb=" O3 NAP D1001 " ideal model delta sigma weight residual 104.94 119.84 -14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O2A NAP B1001 " pdb=" PA NAP B1001 " pdb=" O3 NAP B1001 " ideal model delta sigma weight residual 104.94 119.82 -14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O1A NAP D1001 " pdb=" PA NAP D1001 " pdb=" O2A NAP D1001 " ideal model delta sigma weight residual 121.77 108.05 13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" O1A NAP B1001 " pdb=" PA NAP B1001 " pdb=" O2A NAP B1001 " ideal model delta sigma weight residual 121.77 108.09 13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" C VAL C 654 " pdb=" N GLY C 655 " pdb=" CA GLY C 655 " ideal model delta sigma weight residual 119.98 124.34 -4.36 1.11e+00 8.12e-01 1.54e+01 ... (remaining 25039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 10064 16.23 - 32.46: 745 32.46 - 48.69: 191 48.69 - 64.91: 44 64.91 - 81.14: 12 Dihedral angle restraints: 11056 sinusoidal: 4396 harmonic: 6660 Sorted by residual: dihedral pdb=" CA PRO B 603 " pdb=" C PRO B 603 " pdb=" N LEU B 604 " pdb=" CA LEU B 604 " ideal model delta harmonic sigma weight residual -180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO A 603 " pdb=" C PRO A 603 " pdb=" N LEU A 604 " pdb=" CA LEU A 604 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO C 603 " pdb=" C PRO C 603 " pdb=" N LEU C 604 " pdb=" CA LEU C 604 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 11053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1250 0.043 - 0.085: 835 0.085 - 0.128: 618 0.128 - 0.170: 137 0.170 - 0.213: 8 Chirality restraints: 2848 Sorted by residual: chirality pdb=" C2B NAP B1001 " pdb=" C1B NAP B1001 " pdb=" C3B NAP B1001 " pdb=" O2B NAP B1001 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C2B NAP D1001 " pdb=" C1B NAP D1001 " pdb=" C3B NAP D1001 " pdb=" O2B NAP D1001 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C2B NAP A1001 " pdb=" C1B NAP A1001 " pdb=" C3B NAP A1001 " pdb=" O2B NAP A1001 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2845 not shown) Planarity restraints: 3224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 PNS B1003 " -0.037 2.00e-02 2.50e+03 3.60e-02 1.62e+01 pdb=" C34 PNS B1003 " 0.026 2.00e-02 2.50e+03 pdb=" C37 PNS B1003 " -0.043 2.00e-02 2.50e+03 pdb=" N36 PNS B1003 " 0.051 2.00e-02 2.50e+03 pdb=" O35 PNS B1003 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 531 " 0.187 9.50e-02 1.11e+02 8.41e-02 4.36e+00 pdb=" NE ARG B 531 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 531 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 531 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 531 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 531 " -0.187 9.50e-02 1.11e+02 8.40e-02 4.36e+00 pdb=" NE ARG C 531 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 531 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 531 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 531 " -0.006 2.00e-02 2.50e+03 ... (remaining 3221 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 8846 3.05 - 3.51: 18655 3.51 - 3.97: 28948 3.97 - 4.44: 33738 4.44 - 4.90: 55465 Nonbonded interactions: 145652 Sorted by model distance: nonbonded pdb=" O ALA A 610 " pdb=" OG1 THR A 613 " model vdw 2.582 2.440 nonbonded pdb=" O ALA C 610 " pdb=" OG1 THR C 613 " model vdw 2.583 2.440 nonbonded pdb=" O ALA B 610 " pdb=" OG1 THR B 613 " model vdw 2.584 2.440 nonbonded pdb=" O ALA D 610 " pdb=" OG1 THR D 613 " model vdw 2.584 2.440 nonbonded pdb=" O MET B 525 " pdb=" OG1 THR B 529 " model vdw 2.600 2.440 ... (remaining 145647 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 313 through 902 or resid 1001)) selection = (chain 'B' and (resid 313 through 902 or resid 1001)) selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 6.180 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 48.420 Find NCS groups from input model: 1.280 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.137 18492 Z= 0.636 Angle : 1.283 14.900 25044 Z= 0.860 Chirality : 0.069 0.213 2848 Planarity : 0.005 0.084 3224 Dihedral : 13.025 81.142 6776 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.31 % Favored : 94.00 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.13), residues: 2316 helix: -0.97 (0.13), residues: 912 sheet: -3.37 (0.19), residues: 408 loop : -2.74 (0.15), residues: 996 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 412 time to evaluate : 2.165 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 418 average time/residue: 1.6187 time to fit residues: 743.4134 Evaluate side-chains 231 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 118 optimal weight: 0.0060 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN B 414 ASN ** B 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN D 414 ASN ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 749 GLN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 844 ASN C 414 ASN ** C 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18492 Z= 0.228 Angle : 0.542 9.242 25044 Z= 0.289 Chirality : 0.041 0.175 2848 Planarity : 0.004 0.027 3224 Dihedral : 6.389 59.288 2536 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.24 % Favored : 96.59 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.46 (0.16), residues: 2316 helix: 0.60 (0.15), residues: 960 sheet: -2.25 (0.21), residues: 424 loop : -1.95 (0.17), residues: 932 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 285 time to evaluate : 2.199 Fit side-chains outliers start: 32 outliers final: 4 residues processed: 310 average time/residue: 1.5047 time to fit residues: 516.0984 Evaluate side-chains 227 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.0058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 ASN A 738 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN B 738 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 ASN D 738 ASN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 ASN C 635 GLN C 738 ASN ** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 18492 Z= 0.363 Angle : 0.622 6.718 25044 Z= 0.329 Chirality : 0.045 0.202 2848 Planarity : 0.005 0.039 3224 Dihedral : 6.254 51.614 2536 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 2316 helix: 0.61 (0.16), residues: 968 sheet: -1.66 (0.21), residues: 448 loop : -1.63 (0.18), residues: 900 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 2.011 Fit side-chains outliers start: 42 outliers final: 14 residues processed: 246 average time/residue: 1.8155 time to fit residues: 487.7369 Evaluate side-chains 207 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.6909 time to fit residues: 4.5169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 224 optimal weight: 0.0770 chunk 110 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 overall best weight: 0.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN B 738 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 738 ASN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 18492 Z= 0.139 Angle : 0.445 4.792 25044 Z= 0.239 Chirality : 0.039 0.197 2848 Planarity : 0.003 0.034 3224 Dihedral : 5.697 55.496 2536 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.68 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.29 (0.17), residues: 2316 helix: 1.30 (0.17), residues: 960 sheet: -1.00 (0.22), residues: 476 loop : -1.36 (0.19), residues: 880 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 223 time to evaluate : 2.232 Fit side-chains outliers start: 31 outliers final: 12 residues processed: 245 average time/residue: 1.7192 time to fit residues: 462.7609 Evaluate side-chains 204 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 1.7774 time to fit residues: 4.9602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN B 745 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 18492 Z= 0.290 Angle : 0.544 5.586 25044 Z= 0.288 Chirality : 0.042 0.165 2848 Planarity : 0.004 0.037 3224 Dihedral : 6.178 58.106 2536 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.42 (0.17), residues: 2316 helix: 0.99 (0.16), residues: 960 sheet: -0.82 (0.23), residues: 472 loop : -1.31 (0.19), residues: 884 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 2.156 Fit side-chains outliers start: 38 outliers final: 13 residues processed: 228 average time/residue: 1.6356 time to fit residues: 410.5889 Evaluate side-chains 210 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 1.5164 time to fit residues: 4.4750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 44 optimal weight: 0.0270 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 224 optimal weight: 0.0970 chunk 186 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN A 745 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 738 ASN B 745 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 738 ASN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN C 738 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 18492 Z= 0.190 Angle : 0.474 4.804 25044 Z= 0.254 Chirality : 0.040 0.158 2848 Planarity : 0.004 0.035 3224 Dihedral : 5.957 56.276 2536 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.13 (0.17), residues: 2316 helix: 1.13 (0.17), residues: 972 sheet: -0.56 (0.23), residues: 476 loop : -1.15 (0.19), residues: 868 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 2.074 Fit side-chains outliers start: 31 outliers final: 19 residues processed: 219 average time/residue: 1.6954 time to fit residues: 408.4278 Evaluate side-chains 209 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 2.152 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 1.4611 time to fit residues: 9.4119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 139 optimal weight: 0.0010 chunk 136 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 745 ASN A 787 GLN B 745 ASN B 787 GLN D 787 GLN C 787 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 18492 Z= 0.124 Angle : 0.419 4.456 25044 Z= 0.224 Chirality : 0.038 0.145 2848 Planarity : 0.003 0.032 3224 Dihedral : 5.585 55.417 2536 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.26 (0.17), residues: 2316 helix: 1.47 (0.17), residues: 972 sheet: -0.17 (0.24), residues: 464 loop : -1.08 (0.19), residues: 880 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 223 time to evaluate : 2.264 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 240 average time/residue: 1.6441 time to fit residues: 433.8763 Evaluate side-chains 206 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 2.131 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 2.9555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 67 optimal weight: 0.0270 chunk 43 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 HIS A 635 GLN A 738 ASN A 745 ASN B 522 HIS B 635 GLN B 738 ASN B 745 ASN D 738 ASN D 745 ASN C 522 HIS C 635 GLN C 738 ASN C 745 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 18492 Z= 0.197 Angle : 0.476 4.504 25044 Z= 0.253 Chirality : 0.039 0.150 2848 Planarity : 0.004 0.035 3224 Dihedral : 5.874 54.861 2536 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.37 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.15 (0.17), residues: 2316 helix: 1.31 (0.17), residues: 972 sheet: -0.28 (0.23), residues: 476 loop : -1.02 (0.19), residues: 868 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 2.296 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 216 average time/residue: 1.6150 time to fit residues: 388.0181 Evaluate side-chains 206 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 2.185 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 3.0839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 125 optimal weight: 0.0870 chunk 90 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 745 ASN B 635 GLN B 745 ASN D 745 ASN C 635 GLN C 745 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 18492 Z= 0.257 Angle : 0.526 5.017 25044 Z= 0.280 Chirality : 0.041 0.146 2848 Planarity : 0.004 0.035 3224 Dihedral : 6.138 57.541 2536 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.24 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.05 (0.17), residues: 2316 helix: 1.11 (0.16), residues: 968 sheet: -0.38 (0.23), residues: 476 loop : -1.06 (0.19), residues: 872 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 2.234 Fit side-chains outliers start: 32 outliers final: 18 residues processed: 211 average time/residue: 1.6131 time to fit residues: 376.5084 Evaluate side-chains 205 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 2.234 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.8676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.0570 chunk 134 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN A 745 ASN B 738 ASN B 745 ASN D 738 ASN D 745 ASN C 738 ASN C 745 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 18492 Z= 0.203 Angle : 0.490 4.635 25044 Z= 0.262 Chirality : 0.040 0.156 2848 Planarity : 0.004 0.034 3224 Dihedral : 6.020 55.401 2536 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.04 (0.17), residues: 2316 helix: 1.21 (0.17), residues: 964 sheet: -0.29 (0.23), residues: 476 loop : -1.07 (0.19), residues: 876 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 2.269 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 206 average time/residue: 1.6126 time to fit residues: 366.8347 Evaluate side-chains 204 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.2098 time to fit residues: 3.2245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 745 ASN B 635 GLN B 745 ASN D 745 ASN C 635 GLN C 745 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.160107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128669 restraints weight = 17680.185| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.41 r_work: 0.3140 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 18492 Z= 0.416 Angle : 0.624 5.195 25044 Z= 0.329 Chirality : 0.045 0.147 2848 Planarity : 0.005 0.037 3224 Dihedral : 6.574 58.302 2536 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.50 (0.16), residues: 2316 helix: 0.57 (0.16), residues: 968 sheet: -0.43 (0.24), residues: 444 loop : -1.17 (0.18), residues: 904 =============================================================================== Job complete usr+sys time: 6887.54 seconds wall clock time: 122 minutes 46.37 seconds (7366.37 seconds total)