Starting phenix.real_space_refine on Sat Sep 12 06:45:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n51_0345/09_2026/6n51_0345.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n51_0345/09_2026/6n51_0345.map 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/cci-nas-00/data/ceres_data/6n51_0345/09_2026/6n51_0345.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n51_0345/09_2026/6n51_0345.cif" model { file = "/net/cci-nas-00/data/ceres_data/6n51_0345/09_2026/6n51_0345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n51_0345/09_2026/6n51_0345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n51_0345/09_2026/6n51_0345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n51_0345/09_2026/6n51_0345.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ASP:plan': 4, 'GLU:plan': 8, 'PHE:plan': 4, 'ARG:plan': 3, 'TYR:plan': 4, 'GLN:plan1': 1} 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: {'ASP:plan': 4, 'GLU:plan': 8, 'PHE:plan': 4, 'ARG:plan': 3, 'TYR:plan': 4, 'GLN:plan1': 1} 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: 3.30, per 1000 atoms: 0.23 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 - 3.00 Amino acid : True - 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: 0.72 Conformation dependent library (CDL) restraints added in 522.9 milliseconds 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... Secondary structure from input PDB file: 58 helices and 22 sheets defined 41.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 101 through 119 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) Processing helix chain 'B' and resid 152 through 163 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) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.719A pdb=" N SER B 180 " --> pdb=" O MET B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 209 Processing helix chain 'B' and resid 223 through 236 removed outlier: 4.257A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 257 through 266 removed outlier: 3.843A pdb=" N LEU B 261 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 292 Processing helix chain 'B' and resid 305 through 308 removed outlier: 3.615A pdb=" N ALA B 308 " --> pdb=" O ASP B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.897A pdb=" N VAL B 322 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.541A pdb=" N LEU B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.730A pdb=" N PHE B 363 " --> pdb=" O TRP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.634A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.505A pdb=" N LEU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 602 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 607 through 613 removed outlier: 3.760A pdb=" N LYS B 611 " --> pdb=" O THR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 634 removed outlier: 4.352A pdb=" N CYS B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 669 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) removed outlier: 4.265A pdb=" N ILE B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 Processing helix chain 'B' and resid 689 through 698 Processing helix chain 'B' and resid 701 through 715 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 737 through 758 removed outlier: 3.747A pdb=" N VAL B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) 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 759 through 764 removed outlier: 3.659A pdb=" N ARG B 762 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 794 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 799 through 816 removed outlier: 3.542A pdb=" N CYS B 803 " --> pdb=" O ILE B 799 " (cutoff:3.500A) 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 817 through 824 removed outlier: 3.602A pdb=" N LYS B 821 " --> pdb=" O MET B 817 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 824 " --> pdb=" O PRO B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.527A pdb=" N THR C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 101 through 119 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) Processing helix chain 'A' and resid 152 through 163 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) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.718A pdb=" N SER A 180 " --> pdb=" O MET A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 223 through 236 removed outlier: 4.257A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 257 through 266 removed outlier: 3.843A pdb=" N LEU A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 292 Processing helix chain 'A' and resid 305 through 308 removed outlier: 3.615A pdb=" N ALA A 308 " --> pdb=" O ASP A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.897A pdb=" N VAL A 322 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.540A pdb=" N LEU A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.729A pdb=" N PHE A 363 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.634A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.505A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 602 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 607 through 613 removed outlier: 3.759A pdb=" N LYS A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 634 removed outlier: 4.352A pdb=" N CYS A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 669 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) removed outlier: 4.265A pdb=" N ILE A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 689 through 698 Processing helix chain 'A' and resid 701 through 715 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 737 through 758 removed outlier: 3.747A pdb=" N VAL A 741 " --> pdb=" O ASN A 737 " (cutoff:3.500A) 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 759 through 764 removed outlier: 3.660A pdb=" N ARG A 762 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 794 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 799 through 816 removed outlier: 3.542A pdb=" N CYS A 803 " --> pdb=" O ILE A 799 " (cutoff:3.500A) 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 817 through 824 removed outlier: 3.602A pdb=" N LYS A 821 " --> pdb=" O MET A 817 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 824 " --> pdb=" O PRO A 820 " (cutoff:3.500A) Processing sheet with id=AA1, 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) removed outlier: 7.791A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.632A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 241 through 248 removed outlier: 7.766A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N ALA B 275 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) 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) removed outlier: 6.173A pdb=" N MET B 474 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE B 479 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 446 through 447 removed outlier: 3.555A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 520 through 524 Processing sheet with id=AA7, 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=AA8, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AA9, first strand: chain 'B' and resid 719 through 722 Processing sheet with id=AB1, first strand: chain 'C' and resid 6 through 9 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.535A pdb=" N VAL C 14 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 121 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG C 40 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 9 Processing sheet with id=AB4, 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: 6.833A pdb=" N MET D 36 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 52 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP D 38 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AB5, 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) removed outlier: 7.791A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AB7, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.632A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 241 through 248 removed outlier: 7.766A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) 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) removed outlier: 6.173A pdb=" N MET A 474 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE A 479 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 446 through 447 removed outlier: 3.555A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 520 through 524 Processing sheet with id=AC2, 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) Processing sheet with id=AC3, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AC4, first strand: chain 'A' and resid 719 through 722 574 hydrogen bonds defined for protein. 1593 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: 2.19 Time building geometry restraints manager: 1.01 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=" N14 QUS A 903 " pdb=" O20 QUS A 903 " ideal model delta sigma weight residual 1.431 1.338 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" N14 QUS B 903 " pdb=" O20 QUS B 903 " ideal model delta sigma weight residual 1.431 1.338 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C04 QUS A 903 " pdb=" N14 QUS A 903 " ideal model delta sigma weight residual 1.380 1.320 0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" C04 QUS B 903 " pdb=" N14 QUS B 903 " ideal model delta sigma weight residual 1.380 1.321 0.059 2.00e-02 2.50e+03 8.83e+00 bond pdb=" C04 QUS A 903 " pdb=" N15 QUS A 903 " ideal model delta sigma weight residual 1.383 1.333 0.050 2.00e-02 2.50e+03 6.22e+00 ... (remaining 14394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 19177 2.66 - 5.32: 295 5.32 - 7.98: 39 7.98 - 10.63: 8 10.63 - 13.29: 2 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=" C03 QUS A 903 " pdb=" N14 QUS A 903 " pdb=" O20 QUS A 903 " ideal model delta sigma weight residual 112.77 126.06 -13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C03 QUS B 903 " pdb=" N14 QUS B 903 " pdb=" O20 QUS B 903 " ideal model delta sigma weight residual 112.77 125.90 -13.13 3.00e+00 1.11e-01 1.92e+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 ... (remaining 19516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 8185 15.37 - 30.74: 315 30.74 - 46.11: 83 46.11 - 61.47: 12 61.47 - 76.84: 12 Dihedral angle restraints: 8607 sinusoidal: 3309 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 8604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1590 0.053 - 0.106: 492 0.106 - 0.159: 96 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: 2484 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 2481 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3898 2.80 - 3.32: 12707 3.32 - 3.85: 23078 3.85 - 4.37: 26297 4.37 - 4.90: 44388 Nonbonded interactions: 110368 Sorted by model distance: nonbonded pdb=" OG1 THR A 175 " pdb=" O16 QUS A 903 " model vdw 2.274 3.040 nonbonded pdb=" O LEU A 261 " pdb=" OG1 THR A 265 " model vdw 2.284 3.040 nonbonded pdb=" O LEU B 261 " pdb=" OG1 THR B 265 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR B 175 " pdb=" O16 QUS B 903 " model vdw 2.344 3.040 nonbonded pdb=" O TYR A 629 " pdb=" OG1 THR A 632 " model vdw 2.353 3.040 ... (remaining 110363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 25 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- 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 0.093 14423 Z= 0.274 Angle : 0.868 13.293 19573 Z= 0.463 Chirality : 0.051 0.266 2186 Planarity : 0.006 0.072 2480 Dihedral : 9.734 76.842 5155 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 574 TYR 0.025 0.002 TYR B 317 PHE 0.019 0.002 PHE A 399 TRP 0.030 0.003 TRP A 307 HIS 0.011 0.002 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.27 (14399) covalent geometry : angle 0.86467 / 0.46 (19521) SS BOND : bond 0.00431 / 0.26 ( 20) SS BOND : angle 0.99136 / 0.70 ( 40) hydrogen bonds : bond 0.18278 / 13.17 ( 566) hydrogen bonds : angle 7.42966 / 5.16 ( 1593) link_NAG-ASN : bond 0.00249 / 0.13 ( 4) link_NAG-ASN : angle 2.99591 / 1.54 ( 12) *********************** 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 to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.619 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 REVERT: B 222 ASN cc_start: 0.8935 (p0) cc_final: 0.8600 (p0) REVERT: B 429 MET cc_start: 0.8362 (mpt) cc_final: 0.7839 (mpp) REVERT: B 722 ASP cc_start: 0.8564 (t0) cc_final: 0.8189 (t0) REVERT: C 4 VAL cc_start: 0.9197 (t) cc_final: 0.8995 (p) REVERT: C 22 LEU cc_start: 0.8395 (mt) cc_final: 0.7832 (mm) REVERT: C 45 LYS cc_start: 0.9094 (mttt) cc_final: 0.8843 (pttp) REVERT: C 64 ASP cc_start: 0.8661 (m-30) cc_final: 0.8266 (p0) REVERT: C 83 LEU cc_start: 0.9181 (tp) cc_final: 0.8799 (tp) REVERT: C 109 ASP cc_start: 0.9350 (t0) cc_final: 0.8827 (t70) REVERT: D 6 LEU cc_start: 0.8241 (mt) cc_final: 0.7785 (mt) REVERT: D 22 LEU cc_start: 0.8285 (mt) cc_final: 0.7753 (mm) REVERT: D 83 LEU cc_start: 0.9217 (tp) cc_final: 0.8802 (tp) REVERT: D 109 ASP cc_start: 0.9485 (t0) cc_final: 0.9172 (t0) REVERT: A 106 LEU cc_start: 0.9525 (tp) cc_final: 0.9310 (tp) REVERT: A 722 ASP cc_start: 0.8729 (t0) cc_final: 0.8352 (t70) REVERT: A 778 MET cc_start: 0.9206 (mmm) cc_final: 0.8940 (ttp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1286 time to fit residues: 62.4255 Evaluate side-chains 173 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 46 GLN B 53 HIS B 159 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 HIS ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS A 693 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.094327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.064832 restraints weight = 51373.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066587 restraints weight = 26411.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.067643 restraints weight = 17424.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068347 restraints weight = 13530.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.068666 restraints weight = 11636.910| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14423 Z= 0.168 Angle : 0.640 8.619 19573 Z= 0.328 Chirality : 0.044 0.237 2186 Planarity : 0.004 0.050 2480 Dihedral : 5.917 71.315 2002 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.55 % Allowed : 8.99 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.19), residues: 1818 helix: -0.87 (0.19), residues: 631 sheet: -1.97 (0.28), residues: 308 loop : -1.70 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 29 TYR 0.018 0.001 TYR C 114 PHE 0.024 0.002 PHE D 31 TRP 0.048 0.002 TRP C 107 HIS 0.004 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (14399) covalent geometry : angle 0.63718 / 0.33 (19521) SS BOND : bond 0.00401 / 0.25 ( 20) SS BOND : angle 0.99276 / 0.63 ( 40) hydrogen bonds : bond 0.03761 / 2.62 ( 566) hydrogen bonds : angle 5.29680 / 3.68 ( 1593) link_NAG-ASN : bond 0.00407 / 0.21 ( 4) link_NAG-ASN : angle 2.22899 / 1.17 ( 12) *********************** 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 222 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.564 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: B 31 MET cc_start: 0.8223 (tmm) cc_final: 0.7854 (tmm) REVERT: B 67 GLN cc_start: 0.8596 (mt0) cc_final: 0.8000 (mm-40) REVERT: B 222 ASN cc_start: 0.8918 (p0) cc_final: 0.8299 (p0) REVERT: B 429 MET cc_start: 0.8231 (mpt) cc_final: 0.7930 (mpp) REVERT: B 657 MET cc_start: 0.7590 (ppp) cc_final: 0.6878 (ppp) REVERT: B 720 MET cc_start: 0.8942 (mtp) cc_final: 0.8713 (mtp) REVERT: B 722 ASP cc_start: 0.8589 (t0) cc_final: 0.8164 (t0) REVERT: C 4 VAL cc_start: 0.9149 (t) cc_final: 0.8820 (p) REVERT: C 64 ASP cc_start: 0.8429 (m-30) cc_final: 0.8170 (p0) REVERT: C 75 ASP cc_start: 0.8687 (t0) cc_final: 0.8312 (t0) REVERT: C 79 ASN cc_start: 0.9198 (m-40) cc_final: 0.8841 (t0) REVERT: C 83 LEU cc_start: 0.9063 (tp) cc_final: 0.8695 (tp) REVERT: C 112 TYR cc_start: 0.7726 (m-80) cc_final: 0.7484 (m-80) REVERT: D 6 LEU cc_start: 0.8273 (mt) cc_final: 0.7810 (mt) REVERT: D 75 ASP cc_start: 0.8759 (t0) cc_final: 0.8455 (t0) REVERT: D 83 LEU cc_start: 0.9168 (tp) cc_final: 0.8813 (tp) REVERT: D 109 ASP cc_start: 0.9428 (t0) cc_final: 0.9178 (t0) REVERT: A 31 MET cc_start: 0.8215 (tmm) cc_final: 0.7721 (tmm) REVERT: A 67 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8053 (mm-40) REVERT: A 222 ASN cc_start: 0.8538 (p0) cc_final: 0.8326 (p0) REVERT: A 722 ASP cc_start: 0.8758 (t0) cc_final: 0.8323 (t70) REVERT: A 778 MET cc_start: 0.9304 (mmm) cc_final: 0.8983 (ttp) REVERT: A 818 PHE cc_start: 0.8188 (m-80) cc_final: 0.7921 (m-80) outliers start: 23 outliers final: 9 residues processed: 213 average time/residue: 0.1134 time to fit residues: 36.6317 Evaluate side-chains 164 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 73 optimal weight: 0.0870 chunk 161 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 175 optimal weight: 30.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.092764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063119 restraints weight = 51959.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.064768 restraints weight = 26403.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.065861 restraints weight = 17465.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066296 restraints weight = 13528.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066820 restraints weight = 11969.235| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14423 Z= 0.193 Angle : 0.630 8.182 19573 Z= 0.317 Chirality : 0.044 0.214 2186 Planarity : 0.004 0.044 2480 Dihedral : 5.769 74.346 2002 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.23 % Allowed : 12.03 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1818 helix: 0.00 (0.20), residues: 629 sheet: -1.78 (0.28), residues: 318 loop : -1.57 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 138 TYR 0.015 0.001 TYR B 209 PHE 0.029 0.002 PHE A 399 TRP 0.031 0.002 TRP C 107 HIS 0.005 0.001 HIS C 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (14399) covalent geometry : angle 0.62709 / 0.32 (19521) SS BOND : bond 0.00398 / 0.24 ( 20) SS BOND : angle 0.98929 / 0.71 ( 40) hydrogen bonds : bond 0.03478 / 2.43 ( 566) hydrogen bonds : angle 5.10161 / 3.55 ( 1593) link_NAG-ASN : bond 0.00332 / 0.17 ( 4) link_NAG-ASN : angle 2.04541 / 1.08 ( 12) *********************** 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 200 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8316 (tmm) cc_final: 0.7844 (tmm) REVERT: B 222 ASN cc_start: 0.8797 (p0) cc_final: 0.8475 (p0) REVERT: B 429 MET cc_start: 0.8275 (mpt) cc_final: 0.7907 (mpp) REVERT: B 633 PHE cc_start: 0.6046 (m-80) cc_final: 0.5575 (m-80) REVERT: B 657 MET cc_start: 0.7470 (ppp) cc_final: 0.6784 (ppp) REVERT: B 722 ASP cc_start: 0.8651 (t0) cc_final: 0.8132 (t0) REVERT: C 75 ASP cc_start: 0.8929 (t0) cc_final: 0.8607 (t0) REVERT: C 79 ASN cc_start: 0.9288 (m-40) cc_final: 0.8876 (t0) REVERT: C 83 LEU cc_start: 0.9134 (tp) cc_final: 0.7850 (tp) REVERT: C 112 TYR cc_start: 0.7829 (m-80) cc_final: 0.7494 (m-80) REVERT: D 6 LEU cc_start: 0.8168 (mt) cc_final: 0.7736 (mt) REVERT: D 75 ASP cc_start: 0.9020 (t0) cc_final: 0.8688 (t0) REVERT: D 83 LEU cc_start: 0.9167 (tp) cc_final: 0.7833 (tp) REVERT: D 109 ASP cc_start: 0.9483 (t0) cc_final: 0.9259 (t70) REVERT: A 31 MET cc_start: 0.8341 (tmm) cc_final: 0.7818 (tmm) REVERT: A 67 GLN cc_start: 0.8787 (mt0) cc_final: 0.8472 (mt0) REVERT: A 222 ASN cc_start: 0.8717 (p0) cc_final: 0.8488 (p0) REVERT: A 234 MET cc_start: 0.8836 (mtm) cc_final: 0.8614 (mtm) REVERT: A 720 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8574 (ptp) REVERT: A 722 ASP cc_start: 0.8751 (t0) cc_final: 0.8320 (t70) REVERT: A 778 MET cc_start: 0.9327 (mmm) cc_final: 0.9017 (ttp) outliers start: 33 outliers final: 21 residues processed: 185 average time/residue: 0.1082 time to fit residues: 31.1440 Evaluate side-chains 171 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 119 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 178 optimal weight: 0.0470 chunk 136 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 overall best weight: 3.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.091704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061945 restraints weight = 52190.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063639 restraints weight = 26754.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064719 restraints weight = 17622.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065360 restraints weight = 13756.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.065680 restraints weight = 11849.313| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14423 Z= 0.196 Angle : 0.626 8.350 19573 Z= 0.313 Chirality : 0.044 0.215 2186 Planarity : 0.003 0.042 2480 Dihedral : 5.644 77.498 2002 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.50 % Allowed : 12.84 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.19), residues: 1818 helix: 0.30 (0.20), residues: 631 sheet: -1.62 (0.28), residues: 315 loop : -1.48 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.012 0.001 TYR D 82 PHE 0.019 0.002 PHE B 756 TRP 0.024 0.001 TRP C 107 HIS 0.007 0.001 HIS C 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (14399) covalent geometry : angle 0.62361 / 0.31 (19521) SS BOND : bond 0.00409 / 0.24 ( 20) SS BOND : angle 0.83899 / 0.58 ( 40) hydrogen bonds : bond 0.03325 / 2.32 ( 566) hydrogen bonds : angle 5.01882 / 3.48 ( 1593) link_NAG-ASN : bond 0.00306 / 0.16 ( 4) link_NAG-ASN : angle 2.00924 / 1.07 ( 12) *********************** 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 201 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8205 (tmm) cc_final: 0.7975 (tmm) REVERT: B 222 ASN cc_start: 0.8669 (p0) cc_final: 0.8447 (p0) REVERT: B 429 MET cc_start: 0.8160 (mpt) cc_final: 0.7846 (mpp) REVERT: B 469 MET cc_start: 0.8461 (mmm) cc_final: 0.8164 (mmm) REVERT: B 633 PHE cc_start: 0.5957 (m-80) cc_final: 0.5415 (m-80) REVERT: B 657 MET cc_start: 0.7254 (ppp) cc_final: 0.6572 (ppp) REVERT: B 669 ILE cc_start: 0.7966 (tt) cc_final: 0.7731 (mp) REVERT: B 720 MET cc_start: 0.9126 (mtm) cc_final: 0.8852 (mtp) REVERT: B 722 ASP cc_start: 0.8652 (t0) cc_final: 0.8057 (t0) REVERT: C 75 ASP cc_start: 0.8911 (t0) cc_final: 0.8481 (t0) REVERT: C 79 ASN cc_start: 0.9328 (m-40) cc_final: 0.8864 (t0) REVERT: C 112 TYR cc_start: 0.7764 (m-80) cc_final: 0.7399 (m-80) REVERT: D 6 LEU cc_start: 0.8034 (mt) cc_final: 0.7569 (mt) REVERT: D 75 ASP cc_start: 0.8949 (t0) cc_final: 0.8645 (t0) REVERT: D 83 LEU cc_start: 0.8969 (tp) cc_final: 0.8364 (tp) REVERT: A 31 MET cc_start: 0.8210 (tmm) cc_final: 0.7917 (tmm) REVERT: A 234 MET cc_start: 0.8698 (mtm) cc_final: 0.8460 (mtm) REVERT: A 720 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8589 (ptp) REVERT: A 722 ASP cc_start: 0.8585 (t0) cc_final: 0.8156 (t70) REVERT: A 728 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 778 MET cc_start: 0.9326 (mmm) cc_final: 0.9071 (ttp) outliers start: 37 outliers final: 26 residues processed: 188 average time/residue: 0.1035 time to fit residues: 30.5963 Evaluate side-chains 176 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 28 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 91 optimal weight: 0.0870 chunk 126 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS B 393 GLN A 159 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.093078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.063400 restraints weight = 52024.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065088 restraints weight = 26380.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.066165 restraints weight = 17339.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.066864 restraints weight = 13512.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.067126 restraints weight = 11611.710| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14423 Z= 0.117 Angle : 0.601 13.050 19573 Z= 0.289 Chirality : 0.042 0.213 2186 Planarity : 0.003 0.040 2480 Dihedral : 5.292 71.862 2002 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.50 % Allowed : 13.31 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1818 helix: 0.58 (0.21), residues: 625 sheet: -1.41 (0.29), residues: 315 loop : -1.44 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.009 0.001 TYR A 797 PHE 0.020 0.001 PHE B 756 TRP 0.018 0.001 TRP C 107 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (14399) covalent geometry : angle 0.59905 / 0.29 (19521) SS BOND : bond 0.00332 / 0.21 ( 20) SS BOND : angle 0.65791 / 0.45 ( 40) hydrogen bonds : bond 0.02976 / 2.07 ( 566) hydrogen bonds : angle 4.76613 / 3.30 ( 1593) link_NAG-ASN : bond 0.00359 / 0.18 ( 4) link_NAG-ASN : angle 1.76084 / 0.93 ( 12) *********************** 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 201 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8164 (tmm) cc_final: 0.7957 (tmm) REVERT: B 429 MET cc_start: 0.8165 (mpt) cc_final: 0.7847 (mpp) REVERT: B 633 PHE cc_start: 0.6046 (m-80) cc_final: 0.5523 (m-80) REVERT: B 657 MET cc_start: 0.7503 (ppp) cc_final: 0.6926 (ppp) REVERT: B 722 ASP cc_start: 0.8603 (t0) cc_final: 0.7956 (t0) REVERT: C 75 ASP cc_start: 0.8680 (t0) cc_final: 0.8441 (t0) REVERT: C 79 ASN cc_start: 0.9302 (m-40) cc_final: 0.8868 (t0) REVERT: C 85 MET cc_start: 0.8572 (mpp) cc_final: 0.8085 (mpp) REVERT: C 112 TYR cc_start: 0.7691 (m-80) cc_final: 0.7312 (m-80) REVERT: D 6 LEU cc_start: 0.8101 (mt) cc_final: 0.7673 (mt) REVERT: D 75 ASP cc_start: 0.8857 (t0) cc_final: 0.8577 (t0) REVERT: D 83 LEU cc_start: 0.9031 (tp) cc_final: 0.8663 (tp) REVERT: A 234 MET cc_start: 0.8655 (mtm) cc_final: 0.8319 (mtm) REVERT: A 407 MET cc_start: 0.8914 (tpp) cc_final: 0.8647 (mmm) REVERT: A 722 ASP cc_start: 0.8578 (t0) cc_final: 0.8116 (t70) REVERT: A 728 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: A 778 MET cc_start: 0.9330 (mmm) cc_final: 0.9066 (ttp) outliers start: 37 outliers final: 25 residues processed: 189 average time/residue: 0.0946 time to fit residues: 28.0045 Evaluate side-chains 176 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 63 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 42 optimal weight: 0.0870 overall best weight: 4.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 GLN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** 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 = 0.3687 r_free = 0.3687 target = 0.090465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.060468 restraints weight = 52604.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062154 restraints weight = 26891.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063205 restraints weight = 17721.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063859 restraints weight = 13781.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064203 restraints weight = 11906.745| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14423 Z= 0.250 Angle : 0.702 12.077 19573 Z= 0.345 Chirality : 0.045 0.207 2186 Planarity : 0.004 0.039 2480 Dihedral : 5.733 81.049 2002 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.11 % Allowed : 14.05 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.20), residues: 1818 helix: 0.39 (0.20), residues: 628 sheet: -1.43 (0.29), residues: 309 loop : -1.40 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.011 0.001 TYR B 64 PHE 0.022 0.002 PHE B 756 TRP 0.017 0.002 TRP C 107 HIS 0.005 0.001 HIS C 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (14399) covalent geometry : angle 0.69870 / 0.34 (19521) SS BOND : bond 0.00474 / 0.28 ( 20) SS BOND : angle 1.18327 / 0.92 ( 40) hydrogen bonds : bond 0.03500 / 2.43 ( 566) hydrogen bonds : angle 5.04185 / 3.49 ( 1593) link_NAG-ASN : bond 0.00354 / 0.18 ( 4) link_NAG-ASN : angle 2.05447 / 1.12 ( 12) *********************** 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 197 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8218 (tmm) cc_final: 0.7967 (tmm) REVERT: B 329 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9274 (tt) REVERT: B 429 MET cc_start: 0.8040 (mpt) cc_final: 0.7745 (mpp) REVERT: B 469 MET cc_start: 0.8270 (mmm) cc_final: 0.8004 (mmp) REVERT: B 722 ASP cc_start: 0.8752 (t0) cc_final: 0.8083 (t0) REVERT: C 20 LEU cc_start: 0.8541 (tp) cc_final: 0.8223 (tp) REVERT: C 22 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7671 (mm) REVERT: C 79 ASN cc_start: 0.9307 (m-40) cc_final: 0.8886 (t0) REVERT: C 85 MET cc_start: 0.8507 (mpp) cc_final: 0.8076 (mpp) REVERT: D 6 LEU cc_start: 0.7917 (mt) cc_final: 0.7458 (mt) REVERT: D 75 ASP cc_start: 0.8942 (t0) cc_final: 0.8682 (t0) REVERT: D 83 LEU cc_start: 0.9037 (tp) cc_final: 0.8579 (tp) REVERT: D 112 TYR cc_start: 0.8216 (m-80) cc_final: 0.7636 (m-80) REVERT: A 234 MET cc_start: 0.8719 (mtm) cc_final: 0.8333 (mtm) REVERT: A 722 ASP cc_start: 0.8641 (t0) cc_final: 0.8109 (t70) REVERT: A 728 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: A 778 MET cc_start: 0.9362 (mmm) cc_final: 0.9106 (ttp) outliers start: 46 outliers final: 31 residues processed: 182 average time/residue: 0.0989 time to fit residues: 28.0598 Evaluate side-chains 178 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.093173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063526 restraints weight = 51658.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065216 restraints weight = 25962.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066287 restraints weight = 17010.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.066722 restraints weight = 13208.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.067198 restraints weight = 11707.423| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14423 Z= 0.105 Angle : 0.625 14.743 19573 Z= 0.297 Chirality : 0.043 0.275 2186 Planarity : 0.003 0.038 2480 Dihedral : 5.112 68.150 2002 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.23 % Allowed : 14.59 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.20), residues: 1818 helix: 0.69 (0.21), residues: 629 sheet: -1.05 (0.30), residues: 300 loop : -1.30 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.008 0.001 TYR A 797 PHE 0.022 0.001 PHE B 756 TRP 0.017 0.001 TRP A 532 HIS 0.002 0.000 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (14399) covalent geometry : angle 0.62376 / 0.30 (19521) SS BOND : bond 0.00255 / 0.16 ( 20) SS BOND : angle 0.62956 / 0.42 ( 40) hydrogen bonds : bond 0.02904 / 2.01 ( 566) hydrogen bonds : angle 4.72503 / 3.25 ( 1593) link_NAG-ASN : bond 0.00394 / 0.20 ( 4) link_NAG-ASN : angle 1.70636 / 0.89 ( 12) *********************** 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 195 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8110 (tmm) cc_final: 0.7908 (tmm) REVERT: B 429 MET cc_start: 0.8143 (mpt) cc_final: 0.7819 (mpp) REVERT: B 469 MET cc_start: 0.8282 (mmm) cc_final: 0.8078 (mmp) REVERT: B 722 ASP cc_start: 0.8697 (t0) cc_final: 0.8058 (t0) REVERT: C 20 LEU cc_start: 0.8571 (tp) cc_final: 0.8293 (tp) REVERT: C 22 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7743 (mm) REVERT: C 79 ASN cc_start: 0.9331 (m-40) cc_final: 0.8957 (t0) REVERT: C 82 TYR cc_start: 0.8096 (m-80) cc_final: 0.7895 (m-80) REVERT: C 85 MET cc_start: 0.8636 (mpp) cc_final: 0.8144 (mpp) REVERT: D 6 LEU cc_start: 0.8074 (mt) cc_final: 0.7715 (mt) REVERT: D 59 SER cc_start: 0.8894 (m) cc_final: 0.8687 (p) REVERT: D 83 LEU cc_start: 0.9073 (tp) cc_final: 0.8496 (tp) REVERT: D 112 TYR cc_start: 0.8114 (m-80) cc_final: 0.7563 (m-80) REVERT: D 113 ASP cc_start: 0.9301 (p0) cc_final: 0.9067 (p0) REVERT: A 407 MET cc_start: 0.8947 (tpp) cc_final: 0.8478 (tpt) REVERT: A 722 ASP cc_start: 0.8640 (t0) cc_final: 0.8085 (t0) REVERT: A 728 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 778 MET cc_start: 0.9341 (mmm) cc_final: 0.9027 (ttp) outliers start: 33 outliers final: 25 residues processed: 184 average time/residue: 0.1005 time to fit residues: 29.1919 Evaluate side-chains 170 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 131 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 63 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 chunk 46 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.091912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062236 restraints weight = 51793.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.063931 restraints weight = 26601.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.064973 restraints weight = 17582.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065539 restraints weight = 13741.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.065982 restraints weight = 11969.017| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14423 Z= 0.151 Angle : 0.660 15.239 19573 Z= 0.317 Chirality : 0.043 0.258 2186 Planarity : 0.003 0.067 2480 Dihedral : 5.206 72.945 2002 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.23 % Allowed : 15.68 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.20), residues: 1818 helix: 0.59 (0.21), residues: 645 sheet: -0.99 (0.31), residues: 298 loop : -1.21 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 21 TYR 0.009 0.001 TYR A 187 PHE 0.023 0.001 PHE B 756 TRP 0.019 0.001 TRP B 532 HIS 0.003 0.001 HIS C 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14399) covalent geometry : angle 0.65636 / 0.31 (19521) SS BOND : bond 0.00335 / 0.20 ( 20) SS BOND : angle 1.49297 / 0.77 ( 40) hydrogen bonds : bond 0.03047 / 2.11 ( 566) hydrogen bonds : angle 4.80045 / 3.31 ( 1593) link_NAG-ASN : bond 0.00280 / 0.14 ( 4) link_NAG-ASN : angle 1.68441 / 0.91 ( 12) *********************** 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 184 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8127 (tmm) cc_final: 0.7916 (tmm) REVERT: B 257 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8823 (t80) REVERT: B 329 LEU cc_start: 0.9492 (tp) cc_final: 0.9213 (tt) REVERT: B 429 MET cc_start: 0.8027 (mpt) cc_final: 0.7748 (mpp) REVERT: B 469 MET cc_start: 0.8344 (mmm) cc_final: 0.8043 (mmm) REVERT: B 657 MET cc_start: 0.7067 (tmm) cc_final: 0.5962 (ppp) REVERT: B 722 ASP cc_start: 0.8747 (t0) cc_final: 0.8088 (t0) REVERT: C 20 LEU cc_start: 0.8666 (tp) cc_final: 0.8376 (tp) REVERT: C 22 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7783 (mm) REVERT: C 79 ASN cc_start: 0.9272 (m-40) cc_final: 0.8935 (t0) REVERT: C 85 MET cc_start: 0.8608 (mpp) cc_final: 0.8146 (mpp) REVERT: D 6 LEU cc_start: 0.8034 (mt) cc_final: 0.7694 (mt) REVERT: D 75 ASP cc_start: 0.8822 (t0) cc_final: 0.8542 (t0) REVERT: D 112 TYR cc_start: 0.8137 (m-80) cc_final: 0.7583 (m-80) REVERT: D 113 ASP cc_start: 0.9294 (p0) cc_final: 0.9079 (p0) REVERT: A 234 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8229 (mtm) REVERT: A 407 MET cc_start: 0.8982 (tpp) cc_final: 0.8747 (mmm) REVERT: A 722 ASP cc_start: 0.8672 (t0) cc_final: 0.8118 (p0) REVERT: A 728 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: A 778 MET cc_start: 0.9342 (mmm) cc_final: 0.9104 (ttp) outliers start: 33 outliers final: 25 residues processed: 172 average time/residue: 0.1042 time to fit residues: 27.9776 Evaluate side-chains 174 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 124 optimal weight: 0.0770 chunk 158 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 647 GLN ** 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 = 0.3744 r_free = 0.3744 target = 0.093378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.063692 restraints weight = 51951.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065362 restraints weight = 26112.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066420 restraints weight = 17234.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067103 restraints weight = 13421.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.067428 restraints weight = 11563.929| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14423 Z= 0.107 Angle : 0.648 15.388 19573 Z= 0.306 Chirality : 0.043 0.306 2186 Planarity : 0.003 0.037 2480 Dihedral : 4.945 67.506 2002 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.30 % Allowed : 15.68 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1818 helix: 0.80 (0.21), residues: 633 sheet: -0.80 (0.32), residues: 274 loop : -1.13 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 21 TYR 0.008 0.001 TYR A 797 PHE 0.023 0.001 PHE B 756 TRP 0.017 0.001 TRP C 107 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (14399) covalent geometry : angle 0.64579 / 0.30 (19521) SS BOND : bond 0.00248 / 0.15 ( 20) SS BOND : angle 1.22276 / 0.63 ( 40) hydrogen bonds : bond 0.02754 / 1.91 ( 566) hydrogen bonds : angle 4.61977 / 3.18 ( 1593) link_NAG-ASN : bond 0.00346 / 0.18 ( 4) link_NAG-ASN : angle 1.52146 / 0.80 ( 12) *********************** 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 189 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8090 (tmm) cc_final: 0.7863 (tmm) REVERT: B 257 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8766 (t80) REVERT: B 313 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8505 (p) REVERT: B 329 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9190 (tt) REVERT: B 429 MET cc_start: 0.8066 (mpt) cc_final: 0.7721 (mpp) REVERT: B 469 MET cc_start: 0.8322 (mmm) cc_final: 0.8045 (mmm) REVERT: B 657 MET cc_start: 0.7152 (tmm) cc_final: 0.6180 (ppp) REVERT: B 722 ASP cc_start: 0.8696 (t0) cc_final: 0.8014 (t0) REVERT: C 20 LEU cc_start: 0.8577 (tp) cc_final: 0.8278 (tp) REVERT: C 22 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7801 (mm) REVERT: C 79 ASN cc_start: 0.9304 (m-40) cc_final: 0.9033 (t0) REVERT: C 85 MET cc_start: 0.8597 (mpp) cc_final: 0.8142 (mpp) REVERT: D 6 LEU cc_start: 0.8077 (mt) cc_final: 0.7748 (mt) REVERT: D 82 TYR cc_start: 0.8392 (m-80) cc_final: 0.7810 (m-80) REVERT: D 83 LEU cc_start: 0.9152 (tp) cc_final: 0.8812 (tp) REVERT: D 112 TYR cc_start: 0.8096 (m-80) cc_final: 0.7569 (m-80) REVERT: A 197 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: A 234 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8174 (mtm) REVERT: A 257 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8706 (t80) REVERT: A 407 MET cc_start: 0.8988 (tpp) cc_final: 0.8784 (mmm) REVERT: A 722 ASP cc_start: 0.8639 (t0) cc_final: 0.8107 (p0) REVERT: A 728 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: A 778 MET cc_start: 0.9359 (mmm) cc_final: 0.9139 (ttp) outliers start: 34 outliers final: 20 residues processed: 180 average time/residue: 0.1050 time to fit residues: 29.6812 Evaluate side-chains 169 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 58 optimal weight: 40.0000 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS ** A 360 GLN ** 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 = 0.3721 r_free = 0.3721 target = 0.092265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062560 restraints weight = 51970.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064257 restraints weight = 26754.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065294 restraints weight = 17679.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.065970 restraints weight = 13837.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066290 restraints weight = 11915.272| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14423 Z= 0.138 Angle : 0.673 15.061 19573 Z= 0.314 Chirality : 0.043 0.314 2186 Planarity : 0.003 0.037 2480 Dihedral : 4.965 71.094 2002 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.09 % Allowed : 15.68 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1818 helix: 0.79 (0.21), residues: 635 sheet: -0.73 (0.31), residues: 298 loop : -1.11 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 21 TYR 0.010 0.001 TYR C 114 PHE 0.023 0.001 PHE B 756 TRP 0.017 0.001 TRP C 107 HIS 0.002 0.001 HIS C 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (14399) covalent geometry : angle 0.67162 / 0.31 (19521) SS BOND : bond 0.00331 / 0.21 ( 20) SS BOND : angle 0.69455 / 0.47 ( 40) hydrogen bonds : bond 0.02774 / 1.91 ( 566) hydrogen bonds : angle 4.56524 / 3.14 ( 1593) link_NAG-ASN : bond 0.00246 / 0.13 ( 4) link_NAG-ASN : angle 1.51613 / 0.81 ( 12) ********************** 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 183 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8149 (tmm) cc_final: 0.7885 (tmm) REVERT: B 257 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8831 (t80) REVERT: B 329 LEU cc_start: 0.9498 (tp) cc_final: 0.9229 (tt) REVERT: B 429 MET cc_start: 0.8047 (mpt) cc_final: 0.7740 (mpp) REVERT: B 469 MET cc_start: 0.8307 (mmm) cc_final: 0.7990 (mmm) REVERT: B 657 MET cc_start: 0.7146 (tmm) cc_final: 0.6173 (ppp) REVERT: B 722 ASP cc_start: 0.8705 (t0) cc_final: 0.7999 (t0) REVERT: C 22 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7841 (mm) REVERT: C 85 MET cc_start: 0.8633 (mpp) cc_final: 0.8051 (mpp) REVERT: D 6 LEU cc_start: 0.8082 (mt) cc_final: 0.7757 (mt) REVERT: D 83 LEU cc_start: 0.9117 (tp) cc_final: 0.8782 (tp) REVERT: D 112 TYR cc_start: 0.8066 (m-80) cc_final: 0.7614 (m-80) REVERT: A 197 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: A 222 ASN cc_start: 0.8742 (p0) cc_final: 0.8519 (p0) REVERT: A 234 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8168 (mtm) REVERT: A 257 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8763 (t80) REVERT: A 407 MET cc_start: 0.8987 (tpp) cc_final: 0.8781 (mmm) REVERT: A 722 ASP cc_start: 0.8645 (t0) cc_final: 0.8106 (p0) REVERT: A 728 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 778 MET cc_start: 0.9357 (mmm) cc_final: 0.9141 (ttp) outliers start: 31 outliers final: 22 residues processed: 173 average time/residue: 0.1048 time to fit residues: 28.7210 Evaluate side-chains 172 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 5 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS A 413 ASN ** A 647 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.090709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060793 restraints weight = 51663.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062386 restraints weight = 26264.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063408 restraints weight = 17461.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064019 restraints weight = 13682.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.064363 restraints weight = 11875.925| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14423 Z= 0.212 Angle : 0.720 15.018 19573 Z= 0.344 Chirality : 0.044 0.309 2186 Planarity : 0.004 0.038 2480 Dihedral : 5.344 75.522 2002 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.50 % Allowed : 15.74 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.20), residues: 1818 helix: 0.63 (0.21), residues: 650 sheet: -0.75 (0.31), residues: 288 loop : -1.08 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 21 TYR 0.017 0.001 TYR D 114 PHE 0.023 0.002 PHE B 756 TRP 0.018 0.002 TRP B 532 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (14399) covalent geometry : angle 0.71793 / 0.34 (19521) SS BOND : bond 0.00429 / 0.26 ( 20) SS BOND : angle 0.91180 / 0.60 ( 40) hydrogen bonds : bond 0.03040 / 2.11 ( 566) hydrogen bonds : angle 4.73878 / 3.27 ( 1593) link_NAG-ASN : bond 0.00275 / 0.14 ( 4) link_NAG-ASN : angle 1.82771 / 0.99 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2451.68 seconds wall clock time: 43 minutes 16.24 seconds (2596.24 seconds total)