Starting phenix.real_space_refine on Wed Mar 4 14:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n51_0345/03_2026/6n51_0345.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n51_0345/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6n51_0345/03_2026/6n51_0345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n51_0345/03_2026/6n51_0345.map" model { file = "/net/cci-nas-00/data/ceres_data/6n51_0345/03_2026/6n51_0345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n51_0345/03_2026/6n51_0345.cif" } 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-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.19, 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: 1.20 Conformation dependent library (CDL) restraints added in 530.3 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: 0.39 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: 2.00 Time building geometry restraints manager: 1.64 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: 8261 15.37 - 30.74: 315 30.74 - 46.11: 91 46.11 - 61.47: 12 61.47 - 76.84: 12 Dihedral angle restraints: 8691 sinusoidal: 3393 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 8688 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 13.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 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 : 9.753 76.842 5239 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 covalent geometry : bond 0.00586 (14399) covalent geometry : angle 0.86467 (19521) SS BOND : bond 0.00431 ( 20) SS BOND : angle 0.99136 ( 40) hydrogen bonds : bond 0.18278 ( 566) hydrogen bonds : angle 7.42966 ( 1593) link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 2.99591 ( 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 : 0.502 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: 0.1179 time to fit residues: 57.0574 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 : 0.506 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064945 restraints weight = 51380.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066642 restraints weight = 25955.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067734 restraints weight = 17057.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068190 restraints weight = 13220.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.068612 restraints weight = 11646.234| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2626 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= 0.169 Angle : 0.640 8.424 19573 Z= 0.328 Chirality : 0.044 0.237 2186 Planarity : 0.004 0.050 2480 Dihedral : 6.052 71.470 2086 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.49 % Allowed : 9.19 % Favored : 89.32 % 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: -2.24 (0.19), residues: 1818 helix: -0.86 (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 0.011 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 covalent geometry : bond 0.00370 (14399) covalent geometry : angle 0.63686 (19521) SS BOND : bond 0.00396 ( 20) SS BOND : angle 0.98497 ( 40) hydrogen bonds : bond 0.03739 ( 566) hydrogen bonds : angle 5.30256 ( 1593) link_NAG-ASN : bond 0.00392 ( 4) link_NAG-ASN : angle 2.39365 ( 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: 22 poor density : 200 time to evaluate : 0.543 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: B 31 MET cc_start: 0.8288 (tmm) cc_final: 0.7779 (tmm) REVERT: B 67 GLN cc_start: 0.8693 (mt0) cc_final: 0.8020 (mm-40) REVERT: B 222 ASN cc_start: 0.8961 (p0) cc_final: 0.8273 (p0) REVERT: B 315 ASP cc_start: 0.8408 (m-30) cc_final: 0.8202 (m-30) REVERT: B 429 MET cc_start: 0.8357 (mpt) cc_final: 0.8034 (mpp) REVERT: B 657 MET cc_start: 0.7629 (ppp) cc_final: 0.6936 (ppp) REVERT: B 722 ASP cc_start: 0.8621 (t0) cc_final: 0.8191 (t0) REVERT: C 45 LYS cc_start: 0.9084 (mttt) cc_final: 0.8872 (pttt) REVERT: C 64 ASP cc_start: 0.8575 (m-30) cc_final: 0.8273 (p0) REVERT: C 75 ASP cc_start: 0.8818 (t0) cc_final: 0.8382 (t0) REVERT: C 79 ASN cc_start: 0.9281 (m-40) cc_final: 0.8877 (t0) REVERT: C 83 LEU cc_start: 0.9090 (tp) cc_final: 0.8718 (tp) REVERT: C 112 TYR cc_start: 0.7836 (m-80) cc_final: 0.7548 (m-80) REVERT: D 6 LEU cc_start: 0.8312 (mt) cc_final: 0.7828 (mt) REVERT: D 75 ASP cc_start: 0.8876 (t0) cc_final: 0.8530 (t0) REVERT: D 83 LEU cc_start: 0.9185 (tp) cc_final: 0.7823 (tp) REVERT: D 109 ASP cc_start: 0.9506 (t0) cc_final: 0.9218 (t0) REVERT: A 31 MET cc_start: 0.8278 (tmm) cc_final: 0.7654 (tmm) REVERT: A 67 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8007 (mm-40) REVERT: A 222 ASN cc_start: 0.8569 (p0) cc_final: 0.8339 (p0) REVERT: A 722 ASP cc_start: 0.8800 (t0) cc_final: 0.8354 (t70) REVERT: A 778 MET cc_start: 0.9323 (mmm) cc_final: 0.8987 (ttp) REVERT: A 818 PHE cc_start: 0.8226 (m-80) cc_final: 0.7954 (m-80) outliers start: 22 outliers final: 9 residues processed: 213 average time/residue: 0.1040 time to fit residues: 33.5038 Evaluate side-chains 162 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 9.9990 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 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: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3740 r_free = 0.3740 target = 0.093139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063453 restraints weight = 52023.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065096 restraints weight = 26416.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.066012 restraints weight = 17420.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.066776 restraints weight = 13831.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.067039 restraints weight = 11858.068| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3212 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= 0.178 Angle : 0.619 8.549 19573 Z= 0.310 Chirality : 0.044 0.217 2186 Planarity : 0.003 0.044 2480 Dihedral : 5.835 73.295 2086 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.30 % Allowed : 11.89 % Favored : 85.81 % 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: -1.62 (0.19), residues: 1818 helix: -0.01 (0.20), residues: 629 sheet: -1.73 (0.28), residues: 318 loop : -1.56 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 138 TYR 0.013 0.001 TYR B 209 PHE 0.027 0.001 PHE A 399 TRP 0.031 0.001 TRP C 107 HIS 0.004 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00389 (14399) covalent geometry : angle 0.61651 (19521) SS BOND : bond 0.00451 ( 20) SS BOND : angle 0.87548 ( 40) hydrogen bonds : bond 0.03431 ( 566) hydrogen bonds : angle 5.05447 ( 1593) link_NAG-ASN : bond 0.00305 ( 4) link_NAG-ASN : angle 2.16244 ( 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 202 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.500 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: B 31 MET cc_start: 0.8304 (tmm) cc_final: 0.7833 (tmm) REVERT: B 67 GLN cc_start: 0.8679 (mt0) cc_final: 0.8470 (mt0) REVERT: B 222 ASN cc_start: 0.8757 (p0) cc_final: 0.8367 (p0) REVERT: B 429 MET cc_start: 0.8301 (mpt) cc_final: 0.7926 (mpp) REVERT: B 633 PHE cc_start: 0.6074 (m-80) cc_final: 0.5594 (m-80) REVERT: B 657 MET cc_start: 0.7620 (ppp) cc_final: 0.6979 (ppp) REVERT: B 720 MET cc_start: 0.8984 (mtp) cc_final: 0.8757 (mtp) REVERT: B 722 ASP cc_start: 0.8652 (t0) cc_final: 0.8129 (t0) REVERT: C 45 LYS cc_start: 0.9047 (mttt) cc_final: 0.8834 (pttt) REVERT: C 48 GLU cc_start: 0.7644 (pm20) cc_final: 0.7440 (pm20) REVERT: C 64 ASP cc_start: 0.8619 (m-30) cc_final: 0.8326 (p0) REVERT: C 75 ASP cc_start: 0.8905 (t0) cc_final: 0.8573 (t0) REVERT: C 79 ASN cc_start: 0.9362 (m-40) cc_final: 0.8854 (t0) REVERT: C 83 LEU cc_start: 0.9135 (tp) cc_final: 0.7856 (tp) REVERT: C 112 TYR cc_start: 0.7832 (m-80) cc_final: 0.7494 (m-80) REVERT: D 6 LEU cc_start: 0.8192 (mt) cc_final: 0.7760 (mt) REVERT: D 75 ASP cc_start: 0.9014 (t0) cc_final: 0.8659 (t0) REVERT: D 83 LEU cc_start: 0.8866 (tp) cc_final: 0.8277 (tp) REVERT: D 85 MET cc_start: 0.8628 (mpp) cc_final: 0.7819 (mpp) REVERT: D 109 ASP cc_start: 0.9492 (t0) cc_final: 0.9254 (t70) REVERT: A 31 MET cc_start: 0.8367 (tmm) cc_final: 0.7855 (tmm) REVERT: A 67 GLN cc_start: 0.8756 (mt0) cc_final: 0.8446 (mt0) REVERT: A 222 ASN cc_start: 0.8705 (p0) cc_final: 0.8448 (p0) REVERT: A 234 MET cc_start: 0.8833 (mtm) cc_final: 0.8602 (mtm) REVERT: A 720 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8566 (ptp) REVERT: A 722 ASP cc_start: 0.8744 (t0) cc_final: 0.8313 (t70) REVERT: A 778 MET cc_start: 0.9326 (mmm) cc_final: 0.9013 (ttp) outliers start: 34 outliers final: 20 residues processed: 185 average time/residue: 0.0987 time to fit residues: 28.3067 Evaluate side-chains 175 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 300 LEU 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 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: 8.9990 chunk 125 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS B 769 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.090237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060543 restraints weight = 52503.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062175 restraints weight = 26643.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063213 restraints weight = 17450.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063742 restraints weight = 13588.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064193 restraints weight = 11891.056| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14423 Z= 0.271 Angle : 0.691 7.792 19573 Z= 0.348 Chirality : 0.045 0.226 2186 Planarity : 0.004 0.043 2480 Dihedral : 6.085 80.900 2086 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.64 % Allowed : 13.04 % Favored : 84.32 % 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: -1.48 (0.19), residues: 1818 helix: 0.14 (0.20), residues: 629 sheet: -1.75 (0.28), residues: 316 loop : -1.47 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 29 TYR 0.015 0.002 TYR C 82 PHE 0.021 0.002 PHE A 399 TRP 0.026 0.002 TRP C 107 HIS 0.006 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00586 (14399) covalent geometry : angle 0.68853 (19521) SS BOND : bond 0.00527 ( 20) SS BOND : angle 0.96177 ( 40) hydrogen bonds : bond 0.03668 ( 566) hydrogen bonds : angle 5.20628 ( 1593) link_NAG-ASN : bond 0.00351 ( 4) link_NAG-ASN : angle 2.37061 ( 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 197 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.443 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 31 MET cc_start: 0.8283 (tmm) cc_final: 0.7969 (tmm) REVERT: B 67 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: B 222 ASN cc_start: 0.8759 (p0) cc_final: 0.8503 (p0) REVERT: B 429 MET cc_start: 0.8109 (mpt) cc_final: 0.7765 (mpp) REVERT: B 469 MET cc_start: 0.8558 (mmm) cc_final: 0.7970 (mmm) REVERT: B 657 MET cc_start: 0.7198 (ppp) cc_final: 0.6461 (ppp) REVERT: B 669 ILE cc_start: 0.7911 (tt) cc_final: 0.7671 (mp) REVERT: B 722 ASP cc_start: 0.8666 (t0) cc_final: 0.8076 (t0) REVERT: C 45 LYS cc_start: 0.9013 (mttt) cc_final: 0.8811 (pttt) REVERT: C 48 GLU cc_start: 0.7710 (pm20) cc_final: 0.7103 (pm20) REVERT: C 64 ASP cc_start: 0.8633 (m-30) cc_final: 0.8392 (p0) REVERT: C 75 ASP cc_start: 0.8927 (t0) cc_final: 0.8519 (t0) REVERT: C 79 ASN cc_start: 0.9327 (m-40) cc_final: 0.8889 (t0) REVERT: C 112 TYR cc_start: 0.7738 (m-80) cc_final: 0.7418 (m-80) REVERT: D 6 LEU cc_start: 0.8003 (mt) cc_final: 0.7550 (mt) REVERT: D 75 ASP cc_start: 0.8958 (t0) cc_final: 0.8682 (t0) REVERT: D 83 LEU cc_start: 0.8825 (tp) cc_final: 0.8100 (tp) REVERT: D 85 MET cc_start: 0.8385 (mpp) cc_final: 0.7586 (mpp) REVERT: A 31 MET cc_start: 0.8228 (tmm) cc_final: 0.7948 (tmm) REVERT: A 222 ASN cc_start: 0.8893 (p0) cc_final: 0.8476 (p0) REVERT: A 720 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8616 (ptm) REVERT: A 722 ASP cc_start: 0.8554 (t0) cc_final: 0.8121 (t70) REVERT: A 728 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 778 MET cc_start: 0.9335 (mmm) cc_final: 0.9093 (ttp) outliers start: 39 outliers final: 29 residues processed: 185 average time/residue: 0.0971 time to fit residues: 27.9646 Evaluate side-chains 183 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLN 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 300 LEU Chi-restraints excluded: chain B residue 336 TRP 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 B residue 749 LEU Chi-restraints excluded: chain C residue 4 VAL 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 67 GLN 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 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 673 LEU 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: 8.9990 chunk 141 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.092555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064545 restraints weight = 51884.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.065022 restraints weight = 28717.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065162 restraints weight = 20031.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.065514 restraints weight = 18330.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065661 restraints weight = 16336.396| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14423 Z= 0.126 Angle : 0.607 11.163 19573 Z= 0.293 Chirality : 0.043 0.209 2186 Planarity : 0.003 0.040 2480 Dihedral : 5.473 70.546 2086 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.50 % Allowed : 13.45 % Favored : 84.05 % 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: -1.17 (0.20), residues: 1818 helix: 0.46 (0.21), residues: 631 sheet: -1.45 (0.29), residues: 305 loop : -1.41 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.010 0.001 TYR A 797 PHE 0.021 0.001 PHE B 756 TRP 0.021 0.001 TRP C 107 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00277 (14399) covalent geometry : angle 0.60556 (19521) SS BOND : bond 0.00298 ( 20) SS BOND : angle 0.63894 ( 40) hydrogen bonds : bond 0.03074 ( 566) hydrogen bonds : angle 4.79284 ( 1593) link_NAG-ASN : bond 0.00360 ( 4) link_NAG-ASN : angle 2.00345 ( 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 203 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 429 MET cc_start: 0.8262 (mpt) cc_final: 0.7909 (mpp) REVERT: B 669 ILE cc_start: 0.8023 (tt) cc_final: 0.7806 (mp) REVERT: B 722 ASP cc_start: 0.8669 (t0) cc_final: 0.8023 (t0) REVERT: C 45 LYS cc_start: 0.9067 (mttt) cc_final: 0.8838 (pttp) REVERT: C 64 ASP cc_start: 0.8662 (m-30) cc_final: 0.8374 (p0) REVERT: C 75 ASP cc_start: 0.8826 (t0) cc_final: 0.8535 (t0) REVERT: C 79 ASN cc_start: 0.9365 (m-40) cc_final: 0.8898 (t0) REVERT: C 85 MET cc_start: 0.8719 (mpp) cc_final: 0.8174 (mpp) REVERT: C 112 TYR cc_start: 0.7707 (m-80) cc_final: 0.7320 (m-80) REVERT: D 6 LEU cc_start: 0.8071 (mt) cc_final: 0.7616 (mt) REVERT: D 75 ASP cc_start: 0.9003 (t0) cc_final: 0.8682 (t0) REVERT: D 83 LEU cc_start: 0.8897 (tp) cc_final: 0.8201 (tp) REVERT: D 85 MET cc_start: 0.8588 (mpp) cc_final: 0.7819 (mpp) REVERT: A 722 ASP cc_start: 0.8565 (t0) cc_final: 0.8085 (t70) REVERT: A 728 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 778 MET cc_start: 0.9297 (mmm) cc_final: 0.9011 (ttp) outliers start: 37 outliers final: 25 residues processed: 189 average time/residue: 0.0983 time to fit residues: 28.6744 Evaluate side-chains 174 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 357 GLU Chi-restraints excluded: chain B residue 441 LEU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 63 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 350 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.088430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.058678 restraints weight = 53049.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.060277 restraints weight = 26890.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061301 restraints weight = 17783.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061901 restraints weight = 13839.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062207 restraints weight = 12005.336| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 14423 Z= 0.378 Angle : 0.824 10.826 19573 Z= 0.411 Chirality : 0.048 0.229 2186 Planarity : 0.004 0.040 2480 Dihedral : 6.351 83.129 2086 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.31 % Allowed : 13.72 % Favored : 82.97 % 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: -1.48 (0.19), residues: 1818 helix: 0.14 (0.20), residues: 625 sheet: -1.57 (0.30), residues: 296 loop : -1.56 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 68 TYR 0.013 0.002 TYR A 64 PHE 0.024 0.002 PHE A 399 TRP 0.020 0.002 TRP C 107 HIS 0.007 0.002 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00816 (14399) covalent geometry : angle 0.81860 (19521) SS BOND : bond 0.00616 ( 20) SS BOND : angle 1.86508 ( 40) hydrogen bonds : bond 0.04008 ( 566) hydrogen bonds : angle 5.39832 ( 1593) link_NAG-ASN : bond 0.00504 ( 4) link_NAG-ASN : angle 2.62180 ( 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 200 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 LEU cc_start: 0.9597 (tp) cc_final: 0.9294 (tt) REVERT: B 429 MET cc_start: 0.8030 (mpt) cc_final: 0.7757 (mpp) REVERT: B 469 MET cc_start: 0.8305 (mmm) cc_final: 0.8093 (mmp) REVERT: B 669 ILE cc_start: 0.7919 (tt) cc_final: 0.7680 (mp) REVERT: B 722 ASP cc_start: 0.8755 (t0) cc_final: 0.8112 (t0) REVERT: C 20 LEU cc_start: 0.8722 (tp) cc_final: 0.8440 (tp) REVERT: C 45 LYS cc_start: 0.9029 (mttt) cc_final: 0.8797 (pttt) REVERT: C 48 GLU cc_start: 0.7567 (pm20) cc_final: 0.7356 (pm20) REVERT: C 64 ASP cc_start: 0.8600 (m-30) cc_final: 0.8358 (p0) REVERT: C 85 MET cc_start: 0.8616 (mpp) cc_final: 0.8110 (mpp) REVERT: D 6 LEU cc_start: 0.7961 (mt) cc_final: 0.7569 (mt) REVERT: D 83 LEU cc_start: 0.8922 (tp) cc_final: 0.8668 (tp) REVERT: A 197 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: A 222 ASN cc_start: 0.8897 (p0) cc_final: 0.8493 (p0) REVERT: A 722 ASP cc_start: 0.8660 (t0) cc_final: 0.8049 (p0) REVERT: A 728 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: A 778 MET cc_start: 0.9344 (mmm) cc_final: 0.9112 (ttp) outliers start: 49 outliers final: 38 residues processed: 185 average time/residue: 0.0938 time to fit residues: 26.9283 Evaluate side-chains 183 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 336 TRP Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 786 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 81 VAL Chi-restraints excluded: chain A residue 144 VAL 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 197 GLN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 387 LEU 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 Chi-restraints excluded: chain A residue 791 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** 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 = 0.3696 r_free = 0.3696 target = 0.091066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.061401 restraints weight = 52020.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.063102 restraints weight = 26681.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064195 restraints weight = 17500.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.064865 restraints weight = 13566.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065114 restraints weight = 11679.736| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14423 Z= 0.149 Angle : 0.669 12.407 19573 Z= 0.323 Chirality : 0.044 0.203 2186 Planarity : 0.003 0.040 2480 Dihedral : 5.689 71.153 2086 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.84 % Allowed : 14.66 % Favored : 82.50 % 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: -1.07 (0.20), residues: 1818 helix: 0.53 (0.21), residues: 631 sheet: -1.22 (0.30), residues: 302 loop : -1.42 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 21 TYR 0.009 0.001 TYR D 82 PHE 0.021 0.001 PHE B 756 TRP 0.020 0.001 TRP A 532 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00333 (14399) covalent geometry : angle 0.66590 (19521) SS BOND : bond 0.00395 ( 20) SS BOND : angle 1.13916 ( 40) hydrogen bonds : bond 0.03245 ( 566) hydrogen bonds : angle 4.94608 ( 1593) link_NAG-ASN : bond 0.00343 ( 4) link_NAG-ASN : angle 2.22129 ( 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 196 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 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 257 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8783 (t80) REVERT: B 429 MET cc_start: 0.8066 (mpt) cc_final: 0.7749 (mpp) REVERT: B 669 ILE cc_start: 0.8203 (tt) cc_final: 0.7958 (mp) REVERT: B 722 ASP cc_start: 0.8703 (t0) cc_final: 0.8012 (t0) REVERT: C 22 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7372 (mm) REVERT: C 45 LYS cc_start: 0.9003 (mttt) cc_final: 0.8799 (pttp) REVERT: C 64 ASP cc_start: 0.8516 (m-30) cc_final: 0.8241 (p0) REVERT: C 75 ASP cc_start: 0.8849 (t0) cc_final: 0.8606 (t0) REVERT: C 85 MET cc_start: 0.8426 (mpp) cc_final: 0.8144 (mpp) REVERT: D 6 LEU cc_start: 0.8055 (mt) cc_final: 0.7720 (mt) REVERT: D 75 ASP cc_start: 0.8900 (t0) cc_final: 0.8583 (t0) REVERT: D 83 LEU cc_start: 0.8929 (tp) cc_final: 0.7814 (tp) REVERT: D 85 MET cc_start: 0.8611 (mpp) cc_final: 0.7651 (mpp) REVERT: A 257 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8750 (t80) REVERT: A 313 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8799 (p) REVERT: A 722 ASP cc_start: 0.8671 (t0) cc_final: 0.8078 (t0) REVERT: A 728 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: A 778 MET cc_start: 0.9355 (mmm) cc_final: 0.9106 (ttp) outliers start: 42 outliers final: 31 residues processed: 184 average time/residue: 0.0882 time to fit residues: 25.8708 Evaluate side-chains 181 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 189 MET Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 441 LEU 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 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 151 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 456 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 131 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 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 = 0.3667 r_free = 0.3667 target = 0.089620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059814 restraints weight = 52165.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.061411 restraints weight = 26497.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.062453 restraints weight = 17543.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063074 restraints weight = 13759.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063329 restraints weight = 11902.368| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14423 Z= 0.251 Angle : 0.735 12.061 19573 Z= 0.357 Chirality : 0.045 0.293 2186 Planarity : 0.004 0.038 2480 Dihedral : 5.954 78.731 2086 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.24 % Allowed : 14.66 % 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: -1.09 (0.20), residues: 1818 helix: 0.46 (0.21), residues: 628 sheet: -1.19 (0.31), residues: 295 loop : -1.40 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 21 TYR 0.011 0.001 TYR D 114 PHE 0.022 0.002 PHE B 756 TRP 0.021 0.002 TRP B 532 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00544 (14399) covalent geometry : angle 0.73130 (19521) SS BOND : bond 0.00461 ( 20) SS BOND : angle 1.22410 ( 40) hydrogen bonds : bond 0.03433 ( 566) hydrogen bonds : angle 5.07499 ( 1593) link_NAG-ASN : bond 0.00352 ( 4) link_NAG-ASN : angle 2.33538 ( 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 194 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.539 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: B 31 MET cc_start: 0.8165 (tmm) cc_final: 0.7824 (tmm) REVERT: B 197 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: B 257 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8816 (t80) REVERT: B 313 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8934 (p) REVERT: B 329 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9252 (tt) REVERT: B 429 MET cc_start: 0.7970 (mpt) cc_final: 0.7729 (mpp) REVERT: B 669 ILE cc_start: 0.8202 (tt) cc_final: 0.7971 (mp) REVERT: B 722 ASP cc_start: 0.8750 (t0) cc_final: 0.8066 (t0) REVERT: C 22 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7547 (mm) REVERT: C 45 LYS cc_start: 0.8988 (mttt) cc_final: 0.8771 (pttp) REVERT: C 64 ASP cc_start: 0.8539 (m-30) cc_final: 0.8277 (p0) REVERT: C 85 MET cc_start: 0.8536 (mpp) cc_final: 0.8322 (mpp) REVERT: D 6 LEU cc_start: 0.8035 (mt) cc_final: 0.7702 (mt) REVERT: D 59 SER cc_start: 0.8866 (m) cc_final: 0.8566 (p) REVERT: D 75 ASP cc_start: 0.8939 (t0) cc_final: 0.8708 (t0) REVERT: D 83 LEU cc_start: 0.8973 (tp) cc_final: 0.7831 (tp) REVERT: D 85 MET cc_start: 0.8637 (mpp) cc_final: 0.7565 (mpp) REVERT: D 112 TYR cc_start: 0.8092 (m-80) cc_final: 0.7605 (m-80) REVERT: A 257 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8758 (t80) REVERT: A 313 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8916 (p) REVERT: A 722 ASP cc_start: 0.8668 (t0) cc_final: 0.7990 (p0) REVERT: A 728 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 778 MET cc_start: 0.9381 (mmm) cc_final: 0.9160 (ttp) outliers start: 48 outliers final: 35 residues processed: 180 average time/residue: 0.0932 time to fit residues: 26.4388 Evaluate side-chains 184 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 189 MET Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 273 VAL 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 336 TRP Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 441 LEU 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 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 151 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 456 PHE 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 Chi-restraints excluded: chain A residue 791 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 158 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.092352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.062710 restraints weight = 51898.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.064416 restraints weight = 25994.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.065521 restraints weight = 16990.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.066075 restraints weight = 13151.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.066584 restraints weight = 11448.539| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14423 Z= 0.113 Angle : 0.675 12.513 19573 Z= 0.317 Chirality : 0.043 0.313 2186 Planarity : 0.003 0.037 2480 Dihedral : 5.358 66.125 2086 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.43 % Allowed : 15.74 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.76 (0.20), residues: 1818 helix: 0.71 (0.21), residues: 635 sheet: -1.02 (0.31), residues: 301 loop : -1.19 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 21 TYR 0.017 0.001 TYR D 114 PHE 0.023 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 covalent geometry : bond 0.00254 (14399) covalent geometry : angle 0.67283 (19521) SS BOND : bond 0.00269 ( 20) SS BOND : angle 0.94684 ( 40) hydrogen bonds : bond 0.02919 ( 566) hydrogen bonds : angle 4.70482 ( 1593) link_NAG-ASN : bond 0.00387 ( 4) link_NAG-ASN : angle 1.96512 ( 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 188 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8103 (tmm) cc_final: 0.7731 (tmm) REVERT: B 257 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8870 (t80) REVERT: B 313 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 329 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9200 (tt) REVERT: B 429 MET cc_start: 0.8056 (mpt) cc_final: 0.7757 (mpp) REVERT: B 722 ASP cc_start: 0.8753 (t0) cc_final: 0.8084 (t0) REVERT: C 22 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7653 (mm) REVERT: C 64 ASP cc_start: 0.8477 (m-30) cc_final: 0.8215 (p0) REVERT: C 79 ASN cc_start: 0.9326 (m-40) cc_final: 0.8975 (t0) REVERT: D 6 LEU cc_start: 0.8065 (mt) cc_final: 0.7727 (mt) REVERT: D 82 TYR cc_start: 0.8340 (m-80) cc_final: 0.8131 (m-80) REVERT: D 83 LEU cc_start: 0.8929 (tp) cc_final: 0.7798 (tp) REVERT: D 85 MET cc_start: 0.8617 (mpp) cc_final: 0.7641 (mpp) REVERT: D 112 TYR cc_start: 0.7934 (m-80) cc_final: 0.7495 (m-80) REVERT: A 197 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: A 257 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8770 (t80) REVERT: A 313 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8688 (p) REVERT: A 722 ASP cc_start: 0.8687 (t0) cc_final: 0.8114 (p0) REVERT: A 728 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: A 778 MET cc_start: 0.9362 (mmm) cc_final: 0.9119 (ttp) outliers start: 36 outliers final: 22 residues processed: 177 average time/residue: 0.0881 time to fit residues: 24.7106 Evaluate side-chains 175 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 189 MET 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 325 ILE 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 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 A residue 146 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 414 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 58 optimal weight: 40.0000 chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 111 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.092563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.064928 restraints weight = 51467.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.065214 restraints weight = 27915.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065829 restraints weight = 18645.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066218 restraints weight = 16360.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.066104 restraints weight = 15168.427| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14423 Z= 0.115 Angle : 0.695 15.931 19573 Z= 0.323 Chirality : 0.043 0.305 2186 Planarity : 0.003 0.037 2480 Dihedral : 5.216 67.286 2086 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.23 % Allowed : 16.35 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.86 (0.21), residues: 626 sheet: -0.89 (0.32), residues: 295 loop : -1.09 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 21 TYR 0.017 0.001 TYR D 114 PHE 0.023 0.001 PHE B 756 TRP 0.016 0.001 TRP C 107 HIS 0.002 0.000 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00264 (14399) covalent geometry : angle 0.69050 (19521) SS BOND : bond 0.00223 ( 20) SS BOND : angle 1.60288 ( 40) hydrogen bonds : bond 0.02797 ( 566) hydrogen bonds : angle 4.56782 ( 1593) link_NAG-ASN : bond 0.00335 ( 4) link_NAG-ASN : angle 1.66287 ( 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 187 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8097 (tmm) cc_final: 0.7683 (tmm) REVERT: B 197 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: B 257 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8852 (t80) REVERT: B 313 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8718 (p) REVERT: B 329 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9210 (tt) REVERT: B 429 MET cc_start: 0.8141 (mpt) cc_final: 0.7830 (mpp) REVERT: B 494 MET cc_start: 0.8183 (mtp) cc_final: 0.7968 (mtm) REVERT: B 722 ASP cc_start: 0.8716 (t0) cc_final: 0.8027 (t0) REVERT: C 22 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7516 (mm) REVERT: C 64 ASP cc_start: 0.8676 (m-30) cc_final: 0.8327 (p0) REVERT: D 6 LEU cc_start: 0.8059 (mt) cc_final: 0.7629 (mt) REVERT: D 15 GLN cc_start: 0.9056 (pm20) cc_final: 0.7773 (tp40) REVERT: D 83 LEU cc_start: 0.8915 (tp) cc_final: 0.7902 (tp) REVERT: D 85 MET cc_start: 0.8794 (mpp) cc_final: 0.7847 (mpp) REVERT: D 112 TYR cc_start: 0.7893 (m-80) cc_final: 0.7419 (m-80) REVERT: A 197 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: A 257 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8776 (t80) REVERT: A 313 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8681 (p) REVERT: A 657 MET cc_start: 0.8192 (tmm) cc_final: 0.7175 (ppp) REVERT: A 722 ASP cc_start: 0.8707 (t0) cc_final: 0.8131 (p0) REVERT: A 728 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: A 778 MET cc_start: 0.9344 (mmm) cc_final: 0.9115 (ttp) REVERT: A 814 LEU cc_start: 0.7952 (pp) cc_final: 0.7719 (mp) outliers start: 33 outliers final: 23 residues processed: 177 average time/residue: 0.0886 time to fit residues: 24.9560 Evaluate side-chains 175 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 ILE 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 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 A residue 146 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 414 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 5 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.091994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062322 restraints weight = 51592.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.064017 restraints weight = 26126.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065083 restraints weight = 17185.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065679 restraints weight = 13391.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066150 restraints weight = 11621.842| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14423 Z= 0.132 Angle : 0.704 16.080 19573 Z= 0.326 Chirality : 0.043 0.322 2186 Planarity : 0.003 0.036 2480 Dihedral : 5.196 69.746 2086 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.03 % Allowed : 17.16 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.58 (0.20), residues: 1818 helix: 0.87 (0.21), residues: 624 sheet: -0.89 (0.32), residues: 292 loop : -1.08 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 21 TYR 0.018 0.001 TYR D 114 PHE 0.023 0.001 PHE B 756 TRP 0.017 0.001 TRP C 107 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00300 (14399) covalent geometry : angle 0.70088 (19521) SS BOND : bond 0.00247 ( 20) SS BOND : angle 1.46831 ( 40) hydrogen bonds : bond 0.02804 ( 566) hydrogen bonds : angle 4.56653 ( 1593) link_NAG-ASN : bond 0.00283 ( 4) link_NAG-ASN : angle 1.67094 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.46 seconds wall clock time: 37 minutes 46.51 seconds (2266.51 seconds total)