Starting phenix.real_space_refine (version: dev) on Sat May 14 09:13:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/05_2022/7rlu_24547_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/05_2022/7rlu_24547.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/05_2022/7rlu_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_24547/05_2022/7rlu_24547_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/05_2022/7rlu_24547_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/05_2022/7rlu_24547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/05_2022/7rlu_24547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/05_2022/7rlu_24547_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlu_24547/05_2022/7rlu_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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 21, 'TRANS': 560, 'PCIS': 1} 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: {'PTRANS': 21, 'TRANS': 560, 'PCIS': 1} 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: {'PTRANS': 21, 'TRANS': 560, 'PCIS': 1} 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: {'PTRANS': 21, 'TRANS': 560, 'PCIS': 1} 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: 2 Unresolved non-hydrogen angles: 6 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: 2 Unresolved non-hydrogen angles: 6 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} 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: 10.45, 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: 7.10 Conformation dependent library (CDL) restraints added in 2.6 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: 2.30 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: 5.98 Time building geometry restraints manager: 7.79 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=" C2B NAP D1001 " pdb=" C3B NAP D1001 " ideal model delta sigma weight residual 1.302 1.522 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C2B NAP B1001 " pdb=" C3B NAP B1001 " ideal model delta sigma weight residual 1.302 1.522 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C2B NAP C1001 " pdb=" C3B NAP C1001 " ideal model delta sigma weight residual 1.302 1.521 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C2B NAP A1001 " pdb=" C3B NAP A1001 " ideal model delta sigma weight residual 1.302 1.521 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1B NAP D1001 " pdb=" O4B NAP D1001 " ideal model delta sigma weight residual 1.297 1.434 -0.137 2.00e-02 2.50e+03 4.69e+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=" 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 angle pdb=" C VAL C 633 " pdb=" N GLY C 634 " pdb=" CA GLY C 634 " ideal model delta sigma weight residual 119.98 124.33 -4.35 1.11e+00 8.12e-01 1.54e+01 angle pdb=" C VAL B 654 " pdb=" N GLY B 655 " pdb=" CA GLY B 655 " ideal model delta sigma weight residual 119.98 124.33 -4.35 1.11e+00 8.12e-01 1.53e+01 angle pdb=" C VAL D 633 " pdb=" N GLY D 634 " pdb=" CA GLY D 634 " ideal model delta sigma weight residual 119.98 124.31 -4.33 1.11e+00 8.12e-01 1.53e+01 angle pdb=" C VAL B 633 " pdb=" N GLY B 634 " pdb=" CA GLY B 634 " ideal model delta sigma weight residual 119.98 124.29 -4.31 1.11e+00 8.12e-01 1.51e+01 ... (remaining 25039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 10164 16.23 - 32.46: 747 32.46 - 48.69: 188 48.69 - 64.91: 43 64.91 - 81.14: 10 Dihedral angle restraints: 11152 sinusoidal: 4492 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 11149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1169 0.039 - 0.078: 702 0.078 - 0.118: 751 0.118 - 0.157: 189 0.157 - 0.196: 21 Chirality restraints: 2832 Sorted by residual: chirality pdb=" CB VAL D 338 " pdb=" CA VAL D 338 " pdb=" CG1 VAL D 338 " pdb=" CG2 VAL D 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CB VAL A 338 " pdb=" CA VAL A 338 " pdb=" CG1 VAL A 338 " pdb=" CG2 VAL A 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB VAL B 338 " pdb=" CA VAL B 338 " pdb=" CG1 VAL B 338 " pdb=" CG2 VAL B 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 2829 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 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. 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: 2.020 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: 0.290 Convert atoms to be neutral: 0.150 Process input model: 48.440 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.110 Set refine NCS operators: 0.010 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.220 18492 Z= 0.711 Angle : 1.271 10.372 25044 Z= 0.858 Chirality : 0.069 0.196 2832 Planarity : 0.005 0.084 3224 Dihedral : 12.842 81.142 6872 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.33 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 : 2.080 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 418 average time/residue: 1.4515 time to fit residues: 671.8163 Evaluate side-chains 231 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2331 ------------------------------------------------------------------------------- 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: 4.9990 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: 2.3402 ------------------------------------------------------------------------------- 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: 0.8297 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 18492 Z= 0.266 Angle : 0.576 9.286 25044 Z= 0.304 Chirality : 0.042 0.177 2832 Planarity : 0.004 0.029 3224 Dihedral : 6.095 59.214 2632 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.24 % Favored : 96.59 % Rotamer Outliers : 1.92 % 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: -1.48 (0.16), residues: 2316 helix: 0.57 (0.15), residues: 960 sheet: -2.29 (0.21), residues: 424 loop : -1.94 (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 323 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 286 time to evaluate : 2.130 Fit side-chains outliers start: 37 outliers final: 4 residues processed: 314 average time/residue: 1.3611 time to fit residues: 476.2181 Evaluate side-chains 237 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 2.084 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.0282 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 18492 Z= 0.346 Angle : 0.610 6.559 25044 Z= 0.322 Chirality : 0.045 0.199 2832 Planarity : 0.005 0.038 3224 Dihedral : 5.730 48.217 2632 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.58 % Favored : 96.24 % Rotamer Outliers : 2.12 % 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: -1.11 (0.16), residues: 2316 helix: 0.61 (0.16), residues: 968 sheet: -1.66 (0.20), residues: 472 loop : -1.63 (0.19), residues: 876 *********************** 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 252 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 211 time to evaluate : 2.197 Fit side-chains outliers start: 41 outliers final: 17 residues processed: 250 average time/residue: 1.5586 time to fit residues: 431.1483 Evaluate side-chains 214 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 2.028 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 1.4503 time to fit residues: 6.0513 ------------------------------------------------------------------------------- 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: 9.9990 chunk 158 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 224 optimal weight: 0.2980 chunk 110 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 18492 Z= 0.160 Angle : 0.468 4.897 25044 Z= 0.250 Chirality : 0.040 0.188 2832 Planarity : 0.004 0.036 3224 Dihedral : 5.318 57.466 2632 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % 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: -0.37 (0.17), residues: 2316 helix: 1.21 (0.16), residues: 960 sheet: -0.99 (0.23), residues: 464 loop : -1.41 (0.19), residues: 892 *********************** 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 260 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 2.543 Fit side-chains outliers start: 32 outliers final: 13 residues processed: 252 average time/residue: 1.6034 time to fit residues: 447.8301 Evaluate side-chains 208 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 1.964 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 1.6609 time to fit residues: 6.5466 ------------------------------------------------------------------------------- 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: 0.9980 chunk 127 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- 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 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 18492 Z= 0.428 Angle : 0.642 6.318 25044 Z= 0.337 Chirality : 0.046 0.155 2832 Planarity : 0.005 0.040 3224 Dihedral : 6.085 54.598 2632 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer Outliers : 1.86 % 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: -0.75 (0.16), residues: 2316 helix: 0.53 (0.16), residues: 964 sheet: -0.85 (0.23), residues: 444 loop : -1.35 (0.19), residues: 908 *********************** 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 250 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 2.239 Fit side-chains outliers start: 36 outliers final: 17 residues processed: 238 average time/residue: 1.5418 time to fit residues: 406.2698 Evaluate side-chains 215 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 1.5829 time to fit residues: 8.0321 ------------------------------------------------------------------------------- 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: 0.9980 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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: 0.8337 moved from start: 0.3489 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= 0.218 Angle : 0.509 5.090 25044 Z= 0.271 Chirality : 0.040 0.160 2832 Planarity : 0.004 0.037 3224 Dihedral : 5.689 58.492 2632 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: -0.38 (0.17), residues: 2316 helix: 0.90 (0.16), residues: 968 sheet: -0.60 (0.23), residues: 464 loop : -1.29 (0.19), residues: 884 *********************** 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 248 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 2.072 Fit side-chains outliers start: 38 outliers final: 17 residues processed: 235 average time/residue: 1.4868 time to fit residues: 388.0596 Evaluate side-chains 207 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 2.141 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 2.9491 ------------------------------------------------------------------------------- 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: 0.0570 chunk 163 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 overall best weight: 0.9700 ------------------------------------------------------------------------------- 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 B 738 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 738 ASN D 787 GLN C 738 ASN C 787 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 18492 Z= 0.145 Angle : 0.449 4.523 25044 Z= 0.239 Chirality : 0.038 0.147 2832 Planarity : 0.004 0.033 3224 Dihedral : 5.261 54.121 2632 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % 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: 0.07 (0.17), residues: 2316 helix: 1.26 (0.17), residues: 972 sheet: -0.23 (0.24), residues: 464 loop : -1.13 (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 228 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 2.151 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 222 average time/residue: 1.5681 time to fit residues: 385.4128 Evaluate side-chains 196 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 2.9139 ------------------------------------------------------------------------------- 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: 3.9990 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 142 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8359 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 18492 Z= 0.305 Angle : 0.554 5.281 25044 Z= 0.292 Chirality : 0.042 0.151 2832 Planarity : 0.004 0.038 3224 Dihedral : 5.803 57.053 2632 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 2.02 % 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: -0.28 (0.17), residues: 2316 helix: 0.88 (0.16), residues: 972 sheet: -0.43 (0.23), residues: 472 loop : -1.19 (0.19), residues: 872 *********************** 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 240 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 2.233 Fit side-chains outliers start: 39 outliers final: 17 residues processed: 227 average time/residue: 1.4032 time to fit residues: 355.7512 Evaluate side-chains 211 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 1.4932 time to fit residues: 4.5122 ------------------------------------------------------------------------------- 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: 0.8980 chunk 208 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 635 GLN B 738 ASN B 745 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 738 ASN D 745 ASN C 635 GLN C 738 ASN C 745 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 18492 Z= 0.255 Angle : 0.526 4.880 25044 Z= 0.279 Chirality : 0.041 0.149 2832 Planarity : 0.004 0.035 3224 Dihedral : 5.701 58.510 2632 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.29 % 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: 0.90 (0.16), residues: 972 sheet: -0.33 (0.23), residues: 460 loop : -1.22 (0.18), residues: 884 *********************** 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 211 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 2.104 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 206 average time/residue: 1.5498 time to fit residues: 353.9231 Evaluate side-chains 196 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 2.044 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.8997 ------------------------------------------------------------------------------- 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: 0.8980 chunk 134 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 231 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 chunk 146 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 B 787 GLN D 745 ASN C 635 GLN C 720 HIS C 745 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 18492 Z= 0.129 Angle : 0.441 4.509 25044 Z= 0.236 Chirality : 0.038 0.154 2832 Planarity : 0.004 0.033 3224 Dihedral : 5.153 53.316 2632 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.40 % 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: 0.24 (0.17), residues: 2316 helix: 1.36 (0.17), residues: 972 sheet: -0.01 (0.24), residues: 460 loop : -1.08 (0.19), residues: 884 ********************** 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 233 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 2.403 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 225 average time/residue: 1.5408 time to fit residues: 384.6404 Evaluate side-chains 206 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 2.8384 ------------------------------------------------------------------------------- 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: 0.6980 chunk 56 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 189 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 745 ASN B 720 HIS 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 = 0.3751 r_free = 0.3751 target = 0.163334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129977 restraints weight = 17723.266| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.41 r_work: 0.3314 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work: 0.3188 rms_B_bonded: 2.63 restraints_weight: 0.1250 r_work: 0.3062 rms_B_bonded: 4.66 restraints_weight: 0.0625 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 18492 Z= 0.189 Angle : 0.482 6.109 25044 Z= 0.256 Chirality : 0.039 0.143 2832 Planarity : 0.004 0.034 3224 Dihedral : 5.359 57.815 2632 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: 0.18 (0.17), residues: 2316 helix: 1.28 (0.17), residues: 972 sheet: -0.04 (0.24), residues: 460 loop : -1.06 (0.19), residues: 884 =============================================================================== Job complete usr+sys time: 6149.48 seconds wall clock time: 110 minutes 1.58 seconds (6601.58 seconds total)