Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 05:41:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/04_2023/6n51_0345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/04_2023/6n51_0345.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/04_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_0345/04_2023/6n51_0345_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/04_2023/6n51_0345_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/04_2023/6n51_0345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/04_2023/6n51_0345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/04_2023/6n51_0345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/04_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 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. 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-1.21rc1-4938/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: 7.38, per 1000 atoms: 0.52 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: 5.39 Conformation dependent library (CDL) restraints added in 2.2 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: 1.82 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: 4.28 Time building geometry restraints manager: 5.89 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=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+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: 8183 15.37 - 30.74: 315 30.74 - 46.11: 77 46.11 - 61.47: 6 61.47 - 76.84: 12 Dihedral angle restraints: 8593 sinusoidal: 3295 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 8590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1592 0.053 - 0.106: 492 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 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 4.910 Check model and map are aligned: 0.210 Set scattering table: 0.110 Process input model: 36.480 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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= 0.370 Angle : 0.840 9.779 19521 Z= 0.457 Chirality : 0.051 0.266 2186 Planarity : 0.006 0.072 2478 Dihedral : 9.488 76.842 5141 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.73 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 : 1.611 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: 0.2881 time to fit residues: 137.5449 Evaluate side-chains 167 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2979 ------------------------------------------------------------------------------- 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: 0.8200 moved from start: 0.2832 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= 0.350 Angle : 0.673 7.205 19521 Z= 0.348 Chirality : 0.045 0.234 2186 Planarity : 0.005 0.053 2478 Dihedral : 5.463 67.178 1988 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % 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: -2.30 (0.19), residues: 1818 helix: -0.87 (0.19), residues: 633 sheet: -2.03 (0.29), residues: 305 loop : -1.76 (0.20), residues: 880 *********************** 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 224 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 1.743 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: 210 average time/residue: 0.2699 time to fit residues: 85.6762 Evaluate side-chains 164 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2224 time to fit residues: 11.7211 ------------------------------------------------------------------------------- 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: 4.9990 chunk 51 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 56 optimal weight: 50.0000 chunk 132 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.8269 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 14399 Z= 0.440 Angle : 0.732 9.848 19521 Z= 0.374 Chirality : 0.046 0.218 2186 Planarity : 0.004 0.048 2478 Dihedral : 5.689 76.130 1988 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % 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: -1.94 (0.19), residues: 1818 helix: -0.32 (0.19), residues: 623 sheet: -1.95 (0.28), residues: 306 loop : -1.69 (0.21), residues: 889 *********************** 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 173 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.608 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: 15 residues processed: 165 average time/residue: 0.2717 time to fit residues: 67.4255 Evaluate side-chains 146 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1356 time to fit residues: 6.1588 ------------------------------------------------------------------------------- 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: 5.9990 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 40.0000 chunk 175 optimal weight: 0.0070 chunk 86 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 GLN A 222 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 14399 Z= 0.155 Angle : 0.585 11.030 19521 Z= 0.289 Chirality : 0.042 0.205 2186 Planarity : 0.003 0.045 2478 Dihedral : 4.986 72.376 1988 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 1.55 % 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: -1.42 (0.19), residues: 1818 helix: 0.39 (0.21), residues: 610 sheet: -1.68 (0.29), residues: 309 loop : -1.60 (0.20), 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 190 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 182 average time/residue: 0.2380 time to fit residues: 66.7267 Evaluate side-chains 154 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1320 time to fit residues: 4.9908 ------------------------------------------------------------------------------- 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: 10.0000 chunk 99 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 150 optimal weight: 0.3980 chunk 121 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 157 optimal weight: 0.0670 chunk 44 optimal weight: 0.5980 overall best weight: 1.1720 ------------------------------------------------------------------------------- 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** B 393 GLN B 413 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 415 GLN A 769 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 14399 Z= 0.153 Angle : 0.590 14.361 19521 Z= 0.282 Chirality : 0.042 0.188 2186 Planarity : 0.003 0.043 2478 Dihedral : 4.709 70.538 1988 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 0.95 % 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: -1.15 (0.20), residues: 1818 helix: 0.70 (0.21), residues: 608 sheet: -1.41 (0.30), residues: 304 loop : -1.55 (0.21), residues: 906 *********************** 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 163 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 156 average time/residue: 0.2469 time to fit residues: 59.3386 Evaluate side-chains 141 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1537 time to fit residues: 3.7221 ------------------------------------------------------------------------------- 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: 9.9990 chunk 158 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 C 84 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 14399 Z= 0.242 Angle : 0.614 13.028 19521 Z= 0.300 Chirality : 0.043 0.265 2186 Planarity : 0.003 0.043 2478 Dihedral : 4.836 73.545 1988 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 1.76 % 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: 0.77 (0.21), residues: 605 sheet: -1.38 (0.29), residues: 314 loop : -1.34 (0.21), residues: 899 *********************** 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 164 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 152 average time/residue: 0.2605 time to fit residues: 62.0522 Evaluate side-chains 146 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1420 time to fit residues: 5.6117 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 175 optimal weight: 30.0000 chunk 109 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 14399 Z= 0.271 Angle : 0.651 12.985 19521 Z= 0.315 Chirality : 0.043 0.242 2186 Planarity : 0.003 0.042 2478 Dihedral : 4.954 74.908 1988 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 1.08 % 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: -0.94 (0.20), residues: 1818 helix: 0.72 (0.21), residues: 605 sheet: -1.38 (0.29), residues: 305 loop : -1.26 (0.21), residues: 908 *********************** 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 155 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 148 average time/residue: 0.2453 time to fit residues: 56.8442 Evaluate side-chains 144 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1375 time to fit residues: 4.0308 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 86 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 14399 Z= 0.135 Angle : 0.614 14.491 19521 Z= 0.287 Chirality : 0.042 0.180 2186 Planarity : 0.003 0.041 2478 Dihedral : 4.491 67.938 1988 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.74 % 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: -0.76 (0.20), residues: 1818 helix: 0.91 (0.21), residues: 618 sheet: -1.23 (0.31), residues: 255 loop : -1.26 (0.21), residues: 945 *********************** 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 176 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 169 average time/residue: 0.2443 time to fit residues: 64.1029 Evaluate side-chains 146 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1402 time to fit residues: 3.6905 ------------------------------------------------------------------------------- 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: 50.0000 chunk 168 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 413 ASN B 704 GLN A 159 GLN A 350 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 14399 Z= 0.389 Angle : 0.741 14.015 19521 Z= 0.363 Chirality : 0.046 0.284 2186 Planarity : 0.004 0.040 2478 Dihedral : 5.183 76.393 1988 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % 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: -0.97 (0.20), residues: 1818 helix: 0.41 (0.20), residues: 628 sheet: -1.26 (0.29), residues: 299 loop : -1.14 (0.22), residues: 891 *********************** 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 156 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 150 average time/residue: 0.2380 time to fit residues: 55.5683 Evaluate side-chains 145 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.511 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1495 time to fit residues: 3.6155 ------------------------------------------------------------------------------- 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: 0.9990 chunk 172 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 166 optimal weight: 30.0000 chunk 144 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** B 413 ASN ** A 360 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 14399 Z= 0.178 Angle : 0.680 17.272 19521 Z= 0.315 Chirality : 0.044 0.259 2186 Planarity : 0.003 0.041 2478 Dihedral : 4.793 72.112 1988 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.41 % 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: -0.82 (0.20), residues: 1818 helix: 0.66 (0.21), residues: 629 sheet: -1.18 (0.30), residues: 277 loop : -1.17 (0.21), residues: 912 ********************** 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 153 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 151 average time/residue: 0.2467 time to fit residues: 58.0696 Evaluate side-chains 145 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1546 time to fit residues: 3.4498 ------------------------------------------------------------------------------- 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: 0.3980 chunk 153 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 84 GLN A 222 ASN ** A 360 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.092786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063398 restraints weight = 52104.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065138 restraints weight = 26386.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.066231 restraints weight = 17313.821| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 14399 Z= 0.154 Angle : 0.672 17.429 19521 Z= 0.308 Chirality : 0.043 0.216 2186 Planarity : 0.003 0.040 2478 Dihedral : 4.510 67.690 1988 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.34 % 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: -0.70 (0.20), residues: 1818 helix: 0.81 (0.21), residues: 623 sheet: -1.08 (0.31), residues: 257 loop : -1.14 (0.21), residues: 938 =============================================================================== Job complete usr+sys time: 2495.24 seconds wall clock time: 46 minutes 41.03 seconds (2801.03 seconds total)