Starting phenix.real_space_refine on Thu Sep 26 23:01:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/09_2024/6n51_0345.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/09_2024/6n51_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/09_2024/6n51_0345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/09_2024/6n51_0345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/09_2024/6n51_0345.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/09_2024/6n51_0345.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14087 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6075 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 759} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 6060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6060 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 2, 'QUS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 8.54, per 1000 atoms: 0.61 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: 3.40 Conformation dependent library (CDL) restraints added in 1.6 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3392 Finding SS restraints... 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: 1.37 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: 5.05 Time building geometry restraints manager: 4.02 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 826 or resid 901 through 903)) } ncs_group { reference = (chain 'C' and (resid 3 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 125)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.020 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- 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 14399 Z= 0.387 Angle : 0.865 13.293 19521 Z= 0.462 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 : 5.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.16), residues: 1818 helix: -2.52 (0.15), residues: 614 sheet: -2.32 (0.28), residues: 292 loop : -2.33 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 307 HIS 0.011 0.002 HIS A 53 PHE 0.019 0.002 PHE A 399 TYR 0.025 0.002 TYR B 317 ARG 0.022 0.001 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.551 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: 0.7838 (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: 0.7786 (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: 0.9173 (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: 0.2782 time to fit residues: 132.2745 Evaluate side-chains 173 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.3980 chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 73 optimal weight: 0.0060 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 overall best weight: 2.4802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14399 Z= 0.252 Angle : 0.641 8.224 19521 Z= 0.330 Chirality : 0.044 0.237 2186 Planarity : 0.004 0.050 2480 Dihedral : 6.071 71.948 2086 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.49 % Allowed : 8.92 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.19), residues: 1818 helix: -0.86 (0.19), residues: 632 sheet: -1.93 (0.28), residues: 318 loop : -1.68 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 107 HIS 0.004 0.001 HIS A 361 PHE 0.025 0.002 PHE D 31 TYR 0.018 0.001 TYR C 114 ARG 0.007 0.001 ARG D 29 *********************** 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 220 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 1.638 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: 0.8302 (tmm) cc_final: 0.7772 (tmm) REVERT: B 67 GLN cc_start: 0.8651 (mt0) cc_final: 0.8052 (mm-40) REVERT: B 222 ASN cc_start: 0.8867 (p0) cc_final: 0.8221 (p0) REVERT: B 315 ASP cc_start: 0.8421 (m-30) cc_final: 0.8207 (m-30) REVERT: B 429 MET cc_start: 0.8346 (mpt) cc_final: 0.8034 (mpp) REVERT: B 657 MET cc_start: 0.7623 (ppp) cc_final: 0.6921 (ppp) REVERT: B 722 ASP cc_start: 0.8549 (t0) cc_final: 0.8127 (t0) REVERT: C 45 LYS cc_start: 0.9081 (mttt) cc_final: 0.8872 (pttt) REVERT: C 64 ASP cc_start: 0.8602 (m-30) cc_final: 0.8293 (p0) REVERT: C 75 ASP cc_start: 0.8803 (t0) cc_final: 0.8551 (t0) REVERT: C 79 ASN cc_start: 0.9289 (m-40) cc_final: 0.8873 (t0) REVERT: C 83 LEU cc_start: 0.9096 (tp) cc_final: 0.8727 (tp) REVERT: C 112 TYR cc_start: 0.7865 (m-80) cc_final: 0.7577 (m-80) REVERT: D 6 LEU cc_start: 0.8284 (mt) cc_final: 0.7807 (mt) REVERT: D 75 ASP cc_start: 0.8845 (t0) cc_final: 0.8519 (t0) REVERT: D 83 LEU cc_start: 0.9177 (tp) cc_final: 0.8817 (tp) REVERT: D 109 ASP cc_start: 0.9509 (t0) cc_final: 0.9223 (t0) REVERT: A 31 MET cc_start: 0.8319 (tmm) cc_final: 0.7694 (tmm) REVERT: A 67 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8091 (mm-40) REVERT: A 222 ASN cc_start: 0.8538 (p0) cc_final: 0.8322 (p0) REVERT: A 722 ASP cc_start: 0.8738 (t0) cc_final: 0.8305 (t70) REVERT: A 778 MET cc_start: 0.9307 (mmm) cc_final: 0.8994 (ttp) REVERT: A 818 PHE cc_start: 0.8280 (m-80) cc_final: 0.8008 (m-80) outliers start: 22 outliers final: 8 residues processed: 211 average time/residue: 0.2436 time to fit residues: 76.7409 Evaluate side-chains 161 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 786 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 56 optimal weight: 50.0000 chunk 132 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS ** B 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14399 Z= 0.372 Angle : 0.687 9.100 19521 Z= 0.348 Chirality : 0.045 0.225 2186 Planarity : 0.004 0.044 2480 Dihedral : 6.173 78.011 2086 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.91 % Allowed : 11.89 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.19), residues: 1818 helix: -0.11 (0.20), residues: 633 sheet: -1.90 (0.28), residues: 313 loop : -1.55 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 107 HIS 0.007 0.001 HIS C 61 PHE 0.033 0.002 PHE A 399 TYR 0.019 0.002 TYR B 209 ARG 0.007 0.001 ARG A 138 *********************** 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 203 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 1.492 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: 0.8389 (tmm) cc_final: 0.7911 (tmm) REVERT: B 67 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: B 222 ASN cc_start: 0.8798 (p0) cc_final: 0.8456 (p0) REVERT: B 429 MET cc_start: 0.8262 (mpt) cc_final: 0.7907 (mpp) REVERT: B 657 MET cc_start: 0.7295 (ppp) cc_final: 0.6563 (ppp) REVERT: B 720 MET cc_start: 0.9010 (mtp) cc_final: 0.8808 (mtp) REVERT: B 722 ASP cc_start: 0.8636 (t0) cc_final: 0.8108 (t0) REVERT: C 45 LYS cc_start: 0.9111 (mttt) cc_final: 0.8853 (pttp) REVERT: C 64 ASP cc_start: 0.8730 (m-30) cc_final: 0.8458 (p0) REVERT: C 75 ASP cc_start: 0.8963 (t0) cc_final: 0.8533 (t0) REVERT: C 79 ASN cc_start: 0.9373 (m-40) cc_final: 0.8828 (t0) REVERT: C 83 LEU cc_start: 0.9090 (tp) cc_final: 0.7675 (tp) REVERT: C 112 TYR cc_start: 0.8005 (m-80) cc_final: 0.7619 (m-80) REVERT: D 6 LEU cc_start: 0.8125 (mt) cc_final: 0.7690 (mt) REVERT: D 75 ASP cc_start: 0.9073 (t0) cc_final: 0.8758 (t0) REVERT: D 83 LEU cc_start: 0.9164 (tp) cc_final: 0.7871 (tp) REVERT: A 31 MET cc_start: 0.8433 (tmm) cc_final: 0.7894 (tmm) REVERT: A 67 GLN cc_start: 0.8701 (mt0) cc_final: 0.8411 (mt0) REVERT: A 222 ASN cc_start: 0.8911 (p0) cc_final: 0.8447 (p0) REVERT: A 329 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9429 (tt) REVERT: A 720 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8578 (ptp) REVERT: A 722 ASP cc_start: 0.8596 (t0) cc_final: 0.8184 (t70) REVERT: A 778 MET cc_start: 0.9322 (mmm) cc_final: 0.9035 (ttp) outliers start: 43 outliers final: 26 residues processed: 183 average time/residue: 0.2281 time to fit residues: 63.8329 Evaluate side-chains 179 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 288 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 461 ASP 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 163 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 30.0000 chunk 111 optimal weight: 0.5980 chunk 166 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 157 optimal weight: 0.0670 chunk 47 optimal weight: 0.7980 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14399 Z= 0.143 Angle : 0.569 9.017 19521 Z= 0.280 Chirality : 0.042 0.207 2186 Planarity : 0.003 0.041 2480 Dihedral : 5.387 66.762 2086 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.09 % Allowed : 12.64 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.20), residues: 1818 helix: 0.48 (0.21), residues: 626 sheet: -1.39 (0.29), residues: 314 loop : -1.49 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 107 HIS 0.001 0.000 HIS A 412 PHE 0.019 0.001 PHE B 756 TYR 0.011 0.001 TYR A 797 ARG 0.005 0.000 ARG C 29 *********************** 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 213 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8239 (tmm) cc_final: 0.7974 (tmm) REVERT: B 67 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: B 222 ASN cc_start: 0.8445 (p0) cc_final: 0.8216 (p0) REVERT: B 429 MET cc_start: 0.8274 (mpt) cc_final: 0.7925 (mpp) REVERT: B 633 PHE cc_start: 0.5942 (m-80) cc_final: 0.5475 (m-80) REVERT: B 657 MET cc_start: 0.7573 (ppp) cc_final: 0.6981 (ppp) REVERT: B 722 ASP cc_start: 0.8546 (t0) cc_final: 0.7934 (t0) REVERT: C 64 ASP cc_start: 0.8594 (m-30) cc_final: 0.8239 (p0) REVERT: C 75 ASP cc_start: 0.8882 (t0) cc_final: 0.8470 (t0) REVERT: C 79 ASN cc_start: 0.9400 (m-40) cc_final: 0.8903 (t0) REVERT: C 83 LEU cc_start: 0.8900 (tp) cc_final: 0.8443 (tp) REVERT: C 85 MET cc_start: 0.8635 (mpp) cc_final: 0.7933 (mpp) REVERT: C 112 TYR cc_start: 0.7767 (m-80) cc_final: 0.7406 (m-80) REVERT: D 6 LEU cc_start: 0.8132 (mt) cc_final: 0.7634 (mt) REVERT: D 75 ASP cc_start: 0.8945 (t0) cc_final: 0.8599 (t0) REVERT: D 79 ASN cc_start: 0.9350 (m-40) cc_final: 0.8915 (t0) REVERT: D 83 LEU cc_start: 0.8984 (tp) cc_final: 0.8402 (tp) REVERT: A 31 MET cc_start: 0.8195 (tmm) cc_final: 0.7858 (tmm) REVERT: A 234 MET cc_start: 0.8695 (mtm) cc_final: 0.8473 (mtm) REVERT: A 329 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9381 (tt) REVERT: A 407 MET cc_start: 0.9074 (tpp) cc_final: 0.8766 (mmm) REVERT: A 722 ASP cc_start: 0.8577 (t0) cc_final: 0.7995 (t0) REVERT: A 728 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: A 778 MET cc_start: 0.9321 (mmm) cc_final: 0.9018 (ttp) outliers start: 31 outliers final: 19 residues processed: 201 average time/residue: 0.2276 time to fit residues: 70.0654 Evaluate side-chains 175 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 293 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 161 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 573 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 157 optimal weight: 0.0030 chunk 44 optimal weight: 0.0570 overall best weight: 4.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN B 159 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14399 Z= 0.368 Angle : 0.693 10.143 19521 Z= 0.344 Chirality : 0.045 0.211 2186 Planarity : 0.004 0.039 2480 Dihedral : 5.861 81.353 2086 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.50 % Allowed : 13.92 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.20), residues: 1818 helix: 0.38 (0.20), residues: 625 sheet: -1.49 (0.29), residues: 310 loop : -1.41 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 107 HIS 0.006 0.002 HIS C 61 PHE 0.022 0.002 PHE A 399 TYR 0.012 0.001 TYR B 64 ARG 0.005 0.000 ARG D 47 *********************** 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 187 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8359 (tmm) cc_final: 0.7943 (tmm) REVERT: B 67 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: B 222 ASN cc_start: 0.8725 (p0) cc_final: 0.8438 (p0) REVERT: B 429 MET cc_start: 0.8166 (mpt) cc_final: 0.7869 (mpp) REVERT: B 657 MET cc_start: 0.7286 (ppp) cc_final: 0.6625 (ppp) REVERT: B 722 ASP cc_start: 0.8642 (t0) cc_final: 0.7986 (t0) REVERT: C 53 ILE cc_start: 0.8601 (tt) cc_final: 0.8366 (tt) REVERT: C 64 ASP cc_start: 0.8768 (m-30) cc_final: 0.8507 (p0) REVERT: C 79 ASN cc_start: 0.9389 (m-40) cc_final: 0.8830 (t0) REVERT: C 112 TYR cc_start: 0.7824 (m-80) cc_final: 0.7410 (m-80) REVERT: D 6 LEU cc_start: 0.7948 (mt) cc_final: 0.7474 (mt) REVERT: D 75 ASP cc_start: 0.9119 (t0) cc_final: 0.8802 (t0) REVERT: D 83 LEU cc_start: 0.9080 (tp) cc_final: 0.8788 (tp) REVERT: A 31 MET cc_start: 0.8319 (tmm) cc_final: 0.7975 (tmm) REVERT: A 234 MET cc_start: 0.8813 (mtm) cc_final: 0.8479 (mtm) REVERT: A 329 LEU cc_start: 0.9671 (tp) cc_final: 0.9366 (tt) REVERT: A 407 MET cc_start: 0.9112 (tpp) cc_final: 0.8651 (tpt) REVERT: A 441 LEU cc_start: 0.9520 (mt) cc_final: 0.9289 (mp) REVERT: A 722 ASP cc_start: 0.8565 (t0) cc_final: 0.8074 (t70) REVERT: A 728 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: A 778 MET cc_start: 0.9370 (mmm) cc_final: 0.9116 (ttp) outliers start: 37 outliers final: 26 residues processed: 174 average time/residue: 0.2326 time to fit residues: 62.4345 Evaluate side-chains 169 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14399 Z= 0.400 Angle : 0.730 13.174 19521 Z= 0.360 Chirality : 0.045 0.240 2186 Planarity : 0.004 0.039 2480 Dihedral : 5.998 80.466 2086 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.24 % Allowed : 13.11 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1818 helix: 0.30 (0.20), residues: 627 sheet: -1.45 (0.29), residues: 304 loop : -1.50 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 107 HIS 0.005 0.002 HIS B 101 PHE 0.023 0.002 PHE B 756 TYR 0.011 0.001 TYR B 64 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 149 time to evaluate : 1.441 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: 0.8374 (tmm) cc_final: 0.7972 (tmm) REVERT: B 222 ASN cc_start: 0.8676 (p0) cc_final: 0.8351 (p0) REVERT: B 429 MET cc_start: 0.8160 (mpt) cc_final: 0.7868 (mpp) REVERT: B 722 ASP cc_start: 0.8674 (t0) cc_final: 0.7985 (t0) REVERT: C 64 ASP cc_start: 0.8739 (m-30) cc_final: 0.8457 (p0) REVERT: C 85 MET cc_start: 0.8719 (mpp) cc_final: 0.8050 (mpp) REVERT: D 6 LEU cc_start: 0.7898 (mt) cc_final: 0.7416 (mt) REVERT: D 76 ASN cc_start: 0.8995 (p0) cc_final: 0.8792 (p0) REVERT: D 83 LEU cc_start: 0.9104 (tp) cc_final: 0.8835 (tp) REVERT: A 31 MET cc_start: 0.8304 (tmm) cc_final: 0.7951 (tmm) REVERT: A 197 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: A 234 MET cc_start: 0.8833 (mtm) cc_final: 0.8487 (mtm) REVERT: A 313 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8996 (p) REVERT: A 329 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9334 (tt) REVERT: A 407 MET cc_start: 0.9161 (tpp) cc_final: 0.8731 (tpt) REVERT: A 441 LEU cc_start: 0.9500 (mt) cc_final: 0.9255 (mp) REVERT: A 722 ASP cc_start: 0.8557 (t0) cc_final: 0.8001 (p0) REVERT: A 728 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: A 778 MET cc_start: 0.9367 (mmm) cc_final: 0.9110 (ttp) outliers start: 48 outliers final: 34 residues processed: 182 average time/residue: 0.2343 time to fit residues: 65.1971 Evaluate side-chains 180 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 151 SER Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 414 MET 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 669 ILE 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 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 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14399 Z= 0.374 Angle : 0.720 13.082 19521 Z= 0.355 Chirality : 0.045 0.213 2186 Planarity : 0.004 0.094 2480 Dihedral : 5.976 78.744 2086 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.72 % Allowed : 14.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1818 helix: 0.36 (0.20), residues: 633 sheet: -1.27 (0.30), residues: 300 loop : -1.49 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 532 HIS 0.004 0.002 HIS A 101 PHE 0.021 0.002 PHE B 756 TYR 0.009 0.001 TYR B 317 ARG 0.008 0.001 ARG C 21 *********************** 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 200 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 145 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8369 (tmm) cc_final: 0.7985 (tmm) REVERT: B 197 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: B 222 ASN cc_start: 0.8726 (p0) cc_final: 0.8435 (p0) REVERT: B 257 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8866 (t80) REVERT: B 429 MET cc_start: 0.8097 (mpt) cc_final: 0.7823 (mpp) REVERT: B 722 ASP cc_start: 0.8688 (t0) cc_final: 0.8004 (t0) REVERT: C 20 LEU cc_start: 0.8841 (tp) cc_final: 0.8423 (tp) REVERT: C 64 ASP cc_start: 0.8735 (m-30) cc_final: 0.8451 (p0) REVERT: C 85 MET cc_start: 0.8784 (mpp) cc_final: 0.8134 (mpp) REVERT: D 6 LEU cc_start: 0.7955 (mt) cc_final: 0.7588 (mt) REVERT: D 20 LEU cc_start: 0.8840 (tp) cc_final: 0.8557 (tp) REVERT: D 83 LEU cc_start: 0.8884 (tp) cc_final: 0.7822 (tp) REVERT: D 85 MET cc_start: 0.8607 (mpp) cc_final: 0.7439 (mpp) REVERT: A 31 MET cc_start: 0.8271 (tmm) cc_final: 0.7976 (tmm) REVERT: A 234 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8492 (mtm) REVERT: A 257 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8771 (t80) REVERT: A 313 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8993 (p) REVERT: A 329 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9322 (tt) REVERT: A 407 MET cc_start: 0.9141 (tpp) cc_final: 0.8697 (tpt) REVERT: A 441 LEU cc_start: 0.9515 (mt) cc_final: 0.9217 (mp) REVERT: A 722 ASP cc_start: 0.8595 (t0) cc_final: 0.7952 (p0) REVERT: A 728 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: A 778 MET cc_start: 0.9386 (mmm) cc_final: 0.9164 (ttp) outliers start: 55 outliers final: 39 residues processed: 185 average time/residue: 0.2258 time to fit residues: 63.9375 Evaluate side-chains 187 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 141 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 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 325 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 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 507 ILE 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 21 ARG 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 234 MET 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 329 LEU Chi-restraints excluded: chain A residue 357 GLU 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 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 108 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 16 optimal weight: 0.0000 chunk 137 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 393 GLN B 413 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14399 Z= 0.227 Angle : 0.669 14.018 19521 Z= 0.321 Chirality : 0.044 0.283 2186 Planarity : 0.003 0.083 2480 Dihedral : 5.583 72.326 2086 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.04 % Allowed : 14.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.20), residues: 1818 helix: 0.56 (0.21), residues: 637 sheet: -1.11 (0.31), residues: 296 loop : -1.31 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 532 HIS 0.003 0.001 HIS A 101 PHE 0.022 0.001 PHE B 756 TYR 0.012 0.001 TYR D 114 ARG 0.003 0.000 ARG C 21 *********************** 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 192 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8288 (tmm) cc_final: 0.7970 (tmm) REVERT: B 222 ASN cc_start: 0.8611 (p0) cc_final: 0.8264 (p0) REVERT: B 257 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8881 (t80) REVERT: B 313 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8868 (p) REVERT: B 429 MET cc_start: 0.8144 (mpt) cc_final: 0.7855 (mpp) REVERT: B 722 ASP cc_start: 0.8686 (t0) cc_final: 0.7991 (t0) REVERT: C 21 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6594 (tpp80) REVERT: C 64 ASP cc_start: 0.8688 (m-30) cc_final: 0.8362 (p0) REVERT: C 85 MET cc_start: 0.8729 (mpp) cc_final: 0.8204 (mpp) REVERT: D 6 LEU cc_start: 0.8083 (mt) cc_final: 0.7712 (mt) REVERT: D 75 ASP cc_start: 0.9099 (t0) cc_final: 0.8854 (t0) REVERT: D 82 TYR cc_start: 0.8679 (m-80) cc_final: 0.8472 (m-80) REVERT: D 83 LEU cc_start: 0.8872 (tp) cc_final: 0.7932 (tp) REVERT: D 85 MET cc_start: 0.8724 (mpp) cc_final: 0.7579 (mpp) REVERT: A 197 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: A 234 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8374 (mtm) REVERT: A 257 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8747 (t80) REVERT: A 313 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8858 (p) REVERT: A 329 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9309 (tt) REVERT: A 407 MET cc_start: 0.9063 (tpp) cc_final: 0.8579 (tpt) REVERT: A 441 LEU cc_start: 0.9345 (mt) cc_final: 0.9117 (mp) REVERT: A 657 MET cc_start: 0.7225 (ppp) cc_final: 0.6754 (ppp) REVERT: A 722 ASP cc_start: 0.8581 (t0) cc_final: 0.7979 (p0) REVERT: A 728 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: A 778 MET cc_start: 0.9383 (mmm) cc_final: 0.9140 (ttp) outliers start: 45 outliers final: 26 residues processed: 180 average time/residue: 0.2274 time to fit residues: 62.9941 Evaluate side-chains 173 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 381 CYS 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 21 ARG 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 197 GLN Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 40.0000 chunk 168 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 163 optimal weight: 0.2980 chunk 98 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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 ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14399 Z= 0.297 Angle : 0.707 13.886 19521 Z= 0.339 Chirality : 0.044 0.289 2186 Planarity : 0.004 0.082 2480 Dihedral : 5.702 76.344 2086 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.77 % Allowed : 15.54 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.20), residues: 1818 helix: 0.48 (0.20), residues: 648 sheet: -1.08 (0.31), residues: 291 loop : -1.34 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 532 HIS 0.004 0.001 HIS A 30 PHE 0.023 0.002 PHE B 756 TYR 0.015 0.001 TYR D 114 ARG 0.003 0.000 ARG B 508 *********************** 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 182 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 1.554 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: 0.8333 (tmm) cc_final: 0.7963 (tmm) REVERT: B 197 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: B 222 ASN cc_start: 0.8646 (p0) cc_final: 0.8283 (p0) REVERT: B 257 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8877 (t80) REVERT: B 313 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8917 (p) REVERT: B 429 MET cc_start: 0.8069 (mpt) cc_final: 0.7808 (mpp) REVERT: B 722 ASP cc_start: 0.8660 (t0) cc_final: 0.7944 (t0) REVERT: C 20 LEU cc_start: 0.8925 (tp) cc_final: 0.8634 (tp) REVERT: C 64 ASP cc_start: 0.8714 (m-30) cc_final: 0.8415 (p0) REVERT: C 85 MET cc_start: 0.8797 (mpp) cc_final: 0.8288 (mpp) REVERT: D 6 LEU cc_start: 0.8010 (mt) cc_final: 0.7585 (mt) REVERT: D 75 ASP cc_start: 0.9055 (t0) cc_final: 0.8821 (t0) REVERT: D 83 LEU cc_start: 0.8875 (tp) cc_final: 0.7931 (tp) REVERT: D 85 MET cc_start: 0.8678 (mpp) cc_final: 0.7492 (mpp) REVERT: A 197 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: A 234 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8398 (mtm) REVERT: A 257 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8747 (t80) REVERT: A 313 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8947 (p) REVERT: A 329 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9297 (tt) REVERT: A 722 ASP cc_start: 0.8661 (t0) cc_final: 0.8033 (p0) REVERT: A 728 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 778 MET cc_start: 0.9380 (mmm) cc_final: 0.9166 (ttp) outliers start: 41 outliers final: 28 residues processed: 170 average time/residue: 0.2224 time to fit residues: 59.0315 Evaluate side-chains 175 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE 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 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 234 MET Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 507 ILE 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 107 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14399 Z= 0.178 Angle : 0.670 13.908 19521 Z= 0.315 Chirality : 0.043 0.291 2186 Planarity : 0.003 0.061 2480 Dihedral : 5.263 68.472 2086 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.96 % Allowed : 16.49 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1818 helix: 0.80 (0.21), residues: 636 sheet: -0.90 (0.29), residues: 330 loop : -1.22 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 107 HIS 0.002 0.001 HIS B 101 PHE 0.023 0.001 PHE B 756 TYR 0.012 0.001 TYR D 114 ARG 0.003 0.000 ARG B 138 ********************** 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 177 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 1.613 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: 0.8254 (tmm) cc_final: 0.8044 (tmm) REVERT: B 197 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: B 222 ASN cc_start: 0.8468 (p0) cc_final: 0.8154 (p0) REVERT: B 257 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8840 (t80) REVERT: B 313 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8781 (p) REVERT: B 429 MET cc_start: 0.8140 (mpt) cc_final: 0.7834 (mpp) REVERT: B 722 ASP cc_start: 0.8723 (t0) cc_final: 0.8004 (t0) REVERT: C 20 LEU cc_start: 0.8899 (tp) cc_final: 0.8464 (tp) REVERT: C 64 ASP cc_start: 0.8654 (m-30) cc_final: 0.8345 (p0) REVERT: C 85 MET cc_start: 0.8781 (mpp) cc_final: 0.8273 (mpp) REVERT: D 6 LEU cc_start: 0.8041 (mt) cc_final: 0.7600 (mt) REVERT: D 15 GLN cc_start: 0.8950 (pm20) cc_final: 0.7738 (tp40) REVERT: D 75 ASP cc_start: 0.8990 (t0) cc_final: 0.8670 (t0) REVERT: D 83 LEU cc_start: 0.8895 (tp) cc_final: 0.7950 (tp) REVERT: D 85 MET cc_start: 0.8672 (mpp) cc_final: 0.7537 (mpp) REVERT: A 313 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8739 (p) REVERT: A 329 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9303 (tt) REVERT: A 407 MET cc_start: 0.9122 (tpp) cc_final: 0.8640 (tpt) REVERT: A 441 LEU cc_start: 0.9370 (mp) cc_final: 0.9121 (mp) REVERT: A 722 ASP cc_start: 0.8645 (t0) cc_final: 0.8046 (p0) REVERT: A 728 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: A 778 MET cc_start: 0.9382 (mmm) cc_final: 0.9157 (ttp) outliers start: 29 outliers final: 20 residues processed: 167 average time/residue: 0.2269 time to fit residues: 58.8444 Evaluate side-chains 165 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 197 GLN 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 381 CYS 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 A residue 146 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 414 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 114 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 133 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.093291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064033 restraints weight = 51124.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065718 restraints weight = 25889.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066818 restraints weight = 16933.309| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14399 Z= 0.155 Angle : 0.671 14.003 19521 Z= 0.311 Chirality : 0.042 0.204 2186 Planarity : 0.003 0.043 2480 Dihedral : 5.001 66.399 2086 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.03 % Allowed : 17.03 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1818 helix: 0.79 (0.21), residues: 638 sheet: -0.72 (0.31), residues: 300 loop : -1.08 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 107 HIS 0.002 0.000 HIS C 61 PHE 0.023 0.001 PHE B 756 TYR 0.018 0.001 TYR D 114 ARG 0.005 0.000 ARG B 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2501.63 seconds wall clock time: 45 minutes 44.92 seconds (2744.92 seconds total)