Starting phenix.real_space_refine (version: dev) on Tue Feb 21 07:59:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/02_2023/6n51_0345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/02_2023/6n51_0345.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/02_2023/6n51_0345_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/02_2023/6n51_0345_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/02_2023/6n51_0345_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/02_2023/6n51_0345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/02_2023/6n51_0345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/02_2023/6n51_0345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/02_2023/6n51_0345_updated.pdb" } resolution = 4.0 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 164 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14087 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6075 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 759} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 6060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6060 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 2, 'QUS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 2, 'QUS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.68, per 1000 atoms: 0.55 Number of scatterers: 14087 At special positions: 0 Unit cell: (96.46, 108.12, 203.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 2614 8.00 N 2394 7.00 C 8951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.04 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.02 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.04 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.02 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.02 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG A 902 " - " ASN A 445 " " NAG B 901 " - " ASN B 210 " " NAG B 902 " - " ASN B 445 " Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 1.9 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 20 sheets defined 37.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'B' and resid 66 through 81 Processing helix chain 'B' and resid 102 through 120 removed outlier: 5.202A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.923A pdb=" N ASN B 160 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.257A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 258 through 267 removed outlier: 3.925A pdb=" N SER B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 318 through 321 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.730A pdb=" N PHE B 363 " --> pdb=" O TRP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 418 removed outlier: 3.509A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 4.093A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 601 removed outlier: 3.641A pdb=" N ALA B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 600 " --> pdb=" O PHE B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 612 Processing helix chain 'B' and resid 615 through 633 removed outlier: 3.945A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 668 removed outlier: 4.304A pdb=" N SER B 654 " --> pdb=" O GLY B 650 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 3.923A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS B 665 " --> pdb=" O ALA B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 673 No H-bonds generated for 'chain 'B' and resid 670 through 673' Processing helix chain 'B' and resid 690 through 714 removed outlier: 3.632A pdb=" N ILE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N CYS B 702 " --> pdb=" O PHE B 698 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 705 " --> pdb=" O ILE B 701 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 757 Proline residue: B 743 - end of helix removed outlier: 3.941A pdb=" N TYR B 746 " --> pdb=" O THR B 742 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN B 747 " --> pdb=" O PRO B 743 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 752 " --> pdb=" O GLY B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 763 Processing helix chain 'B' and resid 770 through 793 removed outlier: 4.205A pdb=" N ILE B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP B 785 " --> pdb=" O THR B 781 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 800 through 815 removed outlier: 4.083A pdb=" N VAL B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 removed outlier: 3.568A pdb=" N ILE B 824 " --> pdb=" O PRO B 820 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 825 " --> pdb=" O LYS B 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 102 through 120 removed outlier: 5.203A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.923A pdb=" N ASN A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.257A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 258 through 267 removed outlier: 3.925A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.729A pdb=" N PHE A 363 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.510A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 removed outlier: 4.092A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 601 removed outlier: 3.641A pdb=" N ALA A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 633 removed outlier: 3.945A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 668 removed outlier: 4.304A pdb=" N SER A 654 " --> pdb=" O GLY A 650 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.923A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 690 through 714 removed outlier: 3.632A pdb=" N ILE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N CYS A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 705 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 757 Proline residue: A 743 - end of helix removed outlier: 3.941A pdb=" N TYR A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A 747 " --> pdb=" O PRO A 743 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 752 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 763 Processing helix chain 'A' and resid 770 through 793 removed outlier: 4.205A pdb=" N ILE A 783 " --> pdb=" O TYR A 779 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 800 through 815 removed outlier: 4.083A pdb=" N VAL A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 removed outlier: 3.568A pdb=" N ILE A 824 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE A 825 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 29 through 31 removed outlier: 5.572A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.906A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 324 through 329 removed outlier: 3.548A pdb=" N TRP B 487 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN B 470 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASN B 483 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS B 472 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR B 481 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 520 through 524 Processing sheet with id= F, first strand: chain 'B' and resid 719 through 722 Processing sheet with id= G, first strand: chain 'B' and resid 541 through 545 removed outlier: 3.700A pdb=" N PHE B 544 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 6 through 9 Processing sheet with id= I, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.562A pdb=" N THR C 122 " --> pdb=" O VAL C 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.533A pdb=" N VAL C 121 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 51 through 53 Processing sheet with id= L, first strand: chain 'D' and resid 5 through 9 Processing sheet with id= M, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.576A pdb=" N VAL D 121 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG D 40 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N SER D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.572A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= P, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.906A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 324 through 329 removed outlier: 3.548A pdb=" N TRP A 487 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN A 470 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASN A 483 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS A 472 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR A 481 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 520 through 524 Processing sheet with id= S, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= T, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.700A pdb=" N PHE A 544 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1410 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: 4.46 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2277 1.31 - 1.43: 3843 1.43 - 1.56: 8093 1.56 - 1.68: 0 1.68 - 1.81: 186 Bond restraints: 14399 Sorted by residual: bond pdb=" CB GLN A 159 " pdb=" CG GLN A 159 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.96e+00 bond pdb=" CB GLN B 159 " pdb=" CG GLN B 159 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.95e+00 bond pdb=" CB TRP A 359 " pdb=" CG TRP A 359 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.49e+00 bond pdb=" CB TRP B 359 " pdb=" CG TRP B 359 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.44e+00 bond pdb=" CB TRP A 100 " pdb=" CG TRP A 100 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.95e+00 ... (remaining 14394 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.25: 239 104.25 - 111.70: 6449 111.70 - 119.15: 5136 119.15 - 126.61: 7479 126.61 - 134.06: 218 Bond angle restraints: 19521 Sorted by residual: angle pdb=" C VAL B 499 " pdb=" N TRP B 500 " pdb=" CA TRP B 500 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C VAL A 499 " pdb=" N TRP A 500 " pdb=" CA TRP A 500 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C TYR A 797 " pdb=" N LYS A 798 " pdb=" CA LYS A 798 " ideal model delta sigma weight residual 122.08 128.35 -6.27 1.47e+00 4.63e-01 1.82e+01 angle pdb=" C TYR B 797 " pdb=" N LYS B 798 " pdb=" CA LYS B 798 " ideal model delta sigma weight residual 122.08 128.34 -6.26 1.47e+00 4.63e-01 1.82e+01 angle pdb=" C SER C 49 " pdb=" N VAL C 50 " pdb=" CA VAL C 50 " ideal model delta sigma weight residual 122.97 119.68 3.29 9.80e-01 1.04e+00 1.13e+01 ... (remaining 19516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 8207 15.37 - 30.74: 315 30.74 - 46.11: 77 46.11 - 61.47: 6 61.47 - 76.84: 12 Dihedral angle restraints: 8617 sinusoidal: 3319 harmonic: 5298 Sorted by residual: dihedral pdb=" CB CYS A 419 " pdb=" SG CYS A 419 " pdb=" SG CYS A 426 " pdb=" CB CYS A 426 " ideal model delta sinusoidal sigma weight residual 93.00 164.98 -71.98 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual 93.00 164.97 -71.97 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CA ASN B 222 " pdb=" C ASN B 222 " pdb=" N TYR B 223 " pdb=" CA TYR B 223 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1596 0.053 - 0.106: 488 0.106 - 0.159: 94 0.159 - 0.212: 2 0.212 - 0.266: 6 Chirality restraints: 2186 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 210 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 210 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU B 438 " pdb=" CB LEU B 438 " pdb=" CD1 LEU B 438 " pdb=" CD2 LEU B 438 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2183 not shown) Planarity restraints: 2482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 579 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO B 580 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 580 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 580 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 579 " 0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 580 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 580 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 580 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 159 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" CD GLN B 159 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN B 159 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN B 159 " -0.014 2.00e-02 2.50e+03 ... (remaining 2479 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3911 2.80 - 3.32: 12771 3.32 - 3.85: 23182 3.85 - 4.37: 26397 4.37 - 4.90: 44403 Nonbonded interactions: 110664 Sorted by model distance: nonbonded pdb=" OG1 THR A 175 " pdb=" O16 QUS A 903 " model vdw 2.274 2.440 nonbonded pdb=" O LEU A 261 " pdb=" OG1 THR A 265 " model vdw 2.284 2.440 nonbonded pdb=" O LEU B 261 " pdb=" OG1 THR B 265 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR B 175 " pdb=" O16 QUS B 903 " model vdw 2.344 2.440 nonbonded pdb=" O TYR A 629 " pdb=" OG1 THR A 632 " model vdw 2.353 2.440 ... (remaining 110659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 25 through 826 or resid 901 through 903)) } ncs_group { reference = (chain 'C' and (resid 3 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 125)) 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 8951 2.51 5 N 2394 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.900 Check model and map are aligned: 0.230 Process input model: 36.610 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.006 0.067 14399 Z= 0.366 Angle : 0.836 9.779 19521 Z= 0.457 Chirality : 0.051 0.266 2186 Planarity : 0.006 0.072 2478 Dihedral : 9.480 76.842 5165 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -3.65 (0.16), residues: 1818 helix: -2.52 (0.15), residues: 614 sheet: -2.32 (0.28), residues: 292 loop : -2.33 (0.18), residues: 912 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2907 time to fit residues: 137.8790 Evaluate side-chains 167 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 HIS B 159 GLN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 HIS ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN A 53 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS A 391 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 14399 Z= 0.347 Angle : 0.670 7.180 19521 Z= 0.348 Chirality : 0.045 0.254 2186 Planarity : 0.005 0.053 2478 Dihedral : 5.501 67.012 2012 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.32 (0.19), residues: 1818 helix: -0.88 (0.19), residues: 633 sheet: -2.03 (0.29), residues: 306 loop : -1.77 (0.20), residues: 879 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 209 average time/residue: 0.2462 time to fit residues: 77.7346 Evaluate side-chains 167 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.513 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1241 time to fit residues: 7.1563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 56 optimal weight: 50.0000 chunk 132 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 14399 Z= 0.420 Angle : 0.708 8.670 19521 Z= 0.362 Chirality : 0.045 0.244 2186 Planarity : 0.004 0.048 2478 Dihedral : 5.632 74.449 2012 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.93 (0.19), residues: 1818 helix: -0.32 (0.19), residues: 624 sheet: -1.98 (0.28), residues: 311 loop : -1.67 (0.21), residues: 883 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 165 average time/residue: 0.2643 time to fit residues: 65.4022 Evaluate side-chains 145 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.751 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1300 time to fit residues: 5.3410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 157 optimal weight: 0.0970 chunk 47 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 14399 Z= 0.316 Angle : 0.638 8.870 19521 Z= 0.324 Chirality : 0.044 0.243 2186 Planarity : 0.003 0.046 2478 Dihedral : 5.382 75.202 2012 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.62 (0.19), residues: 1818 helix: 0.11 (0.20), residues: 613 sheet: -1.82 (0.28), residues: 306 loop : -1.62 (0.21), residues: 899 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 168 average time/residue: 0.2450 time to fit residues: 62.3124 Evaluate side-chains 150 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1288 time to fit residues: 5.0298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 0.0870 chunk 72 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 overall best weight: 1.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN B 222 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 769 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14399 Z= 0.185 Angle : 0.600 11.254 19521 Z= 0.292 Chirality : 0.042 0.215 2186 Planarity : 0.003 0.044 2478 Dihedral : 5.005 73.419 2012 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.28 (0.20), residues: 1818 helix: 0.58 (0.21), residues: 607 sheet: -1.60 (0.28), residues: 310 loop : -1.57 (0.21), residues: 901 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 165 average time/residue: 0.2556 time to fit residues: 64.1424 Evaluate side-chains 150 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1426 time to fit residues: 4.9270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 10.0000 chunk 158 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 14399 Z= 0.288 Angle : 0.634 10.415 19521 Z= 0.313 Chirality : 0.043 0.226 2186 Planarity : 0.003 0.042 2478 Dihedral : 5.083 74.596 2012 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.23 (0.20), residues: 1818 helix: 0.50 (0.21), residues: 613 sheet: -1.51 (0.29), residues: 305 loop : -1.48 (0.21), residues: 900 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 159 average time/residue: 0.2467 time to fit residues: 59.9824 Evaluate side-chains 149 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1371 time to fit residues: 4.7669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 148 optimal weight: 0.0270 chunk 98 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 80 optimal weight: 0.0980 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14399 Z= 0.187 Angle : 0.615 13.752 19521 Z= 0.295 Chirality : 0.042 0.268 2186 Planarity : 0.003 0.042 2478 Dihedral : 4.883 72.238 2012 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.97 (0.20), residues: 1818 helix: 0.78 (0.21), residues: 612 sheet: -1.37 (0.29), residues: 305 loop : -1.37 (0.21), residues: 901 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 153 average time/residue: 0.2434 time to fit residues: 57.4613 Evaluate side-chains 146 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1382 time to fit residues: 4.4451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14399 Z= 0.180 Angle : 0.629 13.164 19521 Z= 0.298 Chirality : 0.042 0.269 2186 Planarity : 0.003 0.050 2478 Dihedral : 4.789 71.049 2012 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1818 helix: 0.71 (0.21), residues: 627 sheet: -1.25 (0.29), residues: 307 loop : -1.22 (0.22), residues: 884 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 158 average time/residue: 0.2416 time to fit residues: 59.0688 Evaluate side-chains 147 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1258 time to fit residues: 3.9583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 163 optimal weight: 0.5980 chunk 98 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 704 GLN C 120 GLN D 120 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 14399 Z= 0.387 Angle : 0.741 15.356 19521 Z= 0.364 Chirality : 0.046 0.296 2186 Planarity : 0.004 0.041 2478 Dihedral : 5.353 76.075 2012 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.08 (0.20), residues: 1818 helix: 0.34 (0.20), residues: 627 sheet: -1.24 (0.29), residues: 299 loop : -1.26 (0.21), residues: 892 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 149 average time/residue: 0.2517 time to fit residues: 57.9615 Evaluate side-chains 147 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.642 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1445 time to fit residues: 4.8815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 166 optimal weight: 30.0000 chunk 144 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN C 120 GLN D 120 GLN A 159 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14399 Z= 0.218 Angle : 0.694 16.562 19521 Z= 0.325 Chirality : 0.044 0.288 2186 Planarity : 0.003 0.041 2478 Dihedral : 5.035 73.445 2012 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.85 (0.20), residues: 1818 helix: 0.60 (0.21), residues: 622 sheet: -1.08 (0.30), residues: 279 loop : -1.19 (0.21), residues: 917 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 144 average time/residue: 0.2446 time to fit residues: 54.3356 Evaluate side-chains 138 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.734 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1411 time to fit residues: 2.5270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.0000 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.092962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.063804 restraints weight = 52197.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065472 restraints weight = 26696.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.066544 restraints weight = 17590.797| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14399 Z= 0.154 Angle : 0.680 16.543 19521 Z= 0.311 Chirality : 0.043 0.291 2186 Planarity : 0.003 0.041 2478 Dihedral : 4.654 67.029 2012 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.68 (0.20), residues: 1818 helix: 0.77 (0.21), residues: 623 sheet: -0.88 (0.31), residues: 255 loop : -1.15 (0.21), residues: 940 =============================================================================== Job complete usr+sys time: 2418.05 seconds wall clock time: 45 minutes 9.22 seconds (2709.22 seconds total)