Starting phenix.real_space_refine on Thu Feb 15 13:58:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8j_10124/02_2024/6s8j_10124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8j_10124/02_2024/6s8j_10124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8j_10124/02_2024/6s8j_10124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8j_10124/02_2024/6s8j_10124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8j_10124/02_2024/6s8j_10124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8j_10124/02_2024/6s8j_10124.pdb" } resolution = 2.91 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= 0.008 sd= 0.194 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 57 5.16 5 C 7728 2.51 5 N 2106 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "O TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 523": "OE1" <-> "OE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D ASP 607": "OD1" <-> "OD2" Residue "F GLU 523": "OE1" <-> "OE2" Residue "F ARG 559": "NH1" <-> "NH2" Residue "F ASP 607": "OD1" <-> "OD2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 92": "OD1" <-> "OD2" Residue "Y ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12391 Number of models: 1 Model: "" Number of chains: 27 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 937 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "U" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "D" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "F" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "C" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 937 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "Y" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 937 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Y" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 6.92, per 1000 atoms: 0.56 Number of scatterers: 12391 At special positions: 0 Unit cell: (99.333, 97.635, 122.256, 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 57 16.00 O 2500 8.00 N 2106 7.00 C 7728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=1.99 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 91 " distance=2.04 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 91 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS D 609 " - pdb=" SG CYS C 53 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS E 53 " distance=2.08 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.04 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 98 " distance=2.04 Simple disulfide: pdb=" SG CYS P 105 " - pdb=" SG CYS P 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 98 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 105 " - pdb=" SG CYS Y 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.5 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2820 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 33 sheets defined 14.6% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.931A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.599A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.951A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.700A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.931A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 86 removed outlier: 3.932A pdb=" N GLU U 86 " --> pdb=" O ALA U 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.951A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.700A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.951A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.700A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.599A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.599A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 53 through 57 Processing helix chain 'Y' and resid 28 through 32 Processing helix chain 'Y' and resid 53 through 57 Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLN L 40 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLN L 101 " --> pdb=" O ASP L 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 60 through 62 removed outlier: 5.168A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.705A pdb=" N ALA A 42 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.705A pdb=" N ALA A 42 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AB1, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.388A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 601 through 602 removed outlier: 6.717A pdb=" N CYS B 601 " --> pdb=" O GLU F 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 610 through 611 Processing sheet with id=AB4, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLN O 40 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL O 49 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLN O 101 " --> pdb=" O ASP O 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 18 through 24 Processing sheet with id=AB7, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLN U 40 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL U 49 " --> pdb=" O GLN U 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLN U 101 " --> pdb=" O ASP U 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 18 through 24 Processing sheet with id=AC1, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AC2, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.504A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 42 " --> pdb=" O HIS C 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.504A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 610 through 611 Processing sheet with id=AC5, first strand: chain 'F' and resid 544 through 548 Processing sheet with id=AC6, first strand: chain 'F' and resid 580 through 581 removed outlier: 6.841A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 42 " --> pdb=" O HIS E 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AC8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.388A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AD2, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.388A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'P' and resid 60 through 62 removed outlier: 5.168A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'Y' and resid 60 through 62 removed outlier: 5.169A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4017 1.35 - 1.47: 3208 1.47 - 1.59: 5228 1.59 - 1.72: 0 1.72 - 1.84: 66 Bond restraints: 12519 Sorted by residual: bond pdb=" CG LEU Y 20 " pdb=" CD1 LEU Y 20 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.57e+00 bond pdb=" CG LEU H 20 " pdb=" CD1 LEU H 20 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.53e+00 bond pdb=" CG LEU P 20 " pdb=" CD1 LEU P 20 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.50e+00 bond pdb=" CG GLN O 37 " pdb=" CD GLN O 37 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.00e+00 bond pdb=" CG GLN L 37 " pdb=" CD GLN L 37 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.94e+00 ... (remaining 12514 not shown) Histogram of bond angle deviations from ideal: 101.06 - 107.66: 606 107.66 - 114.25: 6608 114.25 - 120.84: 5345 120.84 - 127.44: 4297 127.44 - 134.03: 151 Bond angle restraints: 17007 Sorted by residual: angle pdb=" N GLY P 101 " pdb=" CA GLY P 101 " pdb=" C GLY P 101 " ideal model delta sigma weight residual 112.34 123.99 -11.65 2.04e+00 2.40e-01 3.26e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 112.34 123.98 -11.64 2.04e+00 2.40e-01 3.26e+01 angle pdb=" N GLY Y 101 " pdb=" CA GLY Y 101 " pdb=" C GLY Y 101 " ideal model delta sigma weight residual 112.34 123.95 -11.61 2.04e+00 2.40e-01 3.24e+01 angle pdb=" N ARG H 100 " pdb=" CA ARG H 100 " pdb=" C ARG H 100 " ideal model delta sigma weight residual 108.52 116.56 -8.04 1.63e+00 3.76e-01 2.43e+01 angle pdb=" N ARG P 100 " pdb=" CA ARG P 100 " pdb=" C ARG P 100 " ideal model delta sigma weight residual 108.52 116.52 -8.00 1.63e+00 3.76e-01 2.41e+01 ... (remaining 17002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 6801 17.35 - 34.70: 505 34.70 - 52.04: 110 52.04 - 69.39: 21 69.39 - 86.74: 18 Dihedral angle restraints: 7455 sinusoidal: 2994 harmonic: 4461 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual -86.00 0.74 -86.74 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 0.73 -86.73 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS E 121 " pdb=" SG CYS E 121 " pdb=" SG CYS E 147 " pdb=" CB CYS E 147 " ideal model delta sinusoidal sigma weight residual -86.00 0.71 -86.71 1 1.00e+01 1.00e-02 9.05e+01 ... (remaining 7452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1798 0.127 - 0.253: 47 0.253 - 0.380: 0 0.380 - 0.507: 0 0.507 - 0.634: 6 Chirality restraints: 1851 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.54e+02 ... (remaining 1848 not shown) Planarity restraints: 2217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 235 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" CD GLU A 235 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU A 235 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A 235 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 235 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" CD GLU C 235 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU C 235 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU C 235 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 235 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" CD GLU E 235 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU E 235 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU E 235 " 0.019 2.00e-02 2.50e+03 ... (remaining 2214 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 756 2.73 - 3.27: 11479 3.27 - 3.81: 18714 3.81 - 4.36: 24579 4.36 - 4.90: 42007 Nonbonded interactions: 97535 Sorted by model distance: nonbonded pdb=" NZ LYS E 114 " pdb=" OD2 ASP Y 56 " model vdw 2.185 2.520 nonbonded pdb=" O GLY Y 101 " pdb=" O HOH Y 301 " model vdw 2.218 2.440 nonbonded pdb=" OE2 GLU H 46 " pdb=" O HOH H 301 " model vdw 2.224 2.440 nonbonded pdb=" O GLY P 101 " pdb=" O HOH P 301 " model vdw 2.229 2.440 nonbonded pdb=" O GLY H 101 " pdb=" O HOH H 302 " model vdw 2.245 2.440 ... (remaining 97530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.140 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.100 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 0.078 12519 Z= 0.398 Angle : 0.996 11.647 17007 Z= 0.545 Chirality : 0.064 0.634 1851 Planarity : 0.006 0.052 2214 Dihedral : 13.159 85.274 4563 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.28 % Favored : 96.53 % Rotamer: Outliers : 3.27 % Allowed : 5.69 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.19), residues: 1554 helix: 0.15 (0.41), residues: 144 sheet: 0.05 (0.21), residues: 555 loop : -0.86 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 114 HIS 0.027 0.005 HIS D 602 PHE 0.033 0.003 PHE H 70 TYR 0.021 0.003 TYR L 94 ARG 0.028 0.002 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 271 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8048 (pttt) cc_final: 0.7800 (pttm) REVERT: L 75 SER cc_start: 0.8085 (OUTLIER) cc_final: 0.7869 (p) REVERT: H 43 LYS cc_start: 0.7623 (mppt) cc_final: 0.7272 (mmtm) REVERT: A 65 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8438 (t) REVERT: A 140 LYS cc_start: 0.8382 (tttt) cc_final: 0.7948 (mtpp) REVERT: A 216 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7834 (m) REVERT: B 567 GLN cc_start: 0.8650 (tt0) cc_final: 0.8367 (tt0) REVERT: B 583 SER cc_start: 0.9027 (p) cc_final: 0.8709 (t) REVERT: B 587 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7423 (ttm110) REVERT: U 48 LYS cc_start: 0.8196 (pttt) cc_final: 0.7976 (pttm) REVERT: D 556 CYS cc_start: 0.7019 (m) cc_final: 0.6673 (m) REVERT: D 587 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7372 (ttm110) REVERT: F 587 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7495 (ttm110) REVERT: C 84 LYS cc_start: 0.8598 (mttt) cc_final: 0.8392 (mtmt) REVERT: C 150 ASP cc_start: 0.7030 (m-30) cc_final: 0.6715 (m-30) REVERT: E 140 LYS cc_start: 0.8446 (tttt) cc_final: 0.8142 (mtpp) REVERT: Y 91 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6561 (pm20) outliers start: 42 outliers final: 6 residues processed: 307 average time/residue: 1.2209 time to fit residues: 406.7433 Evaluate side-chains 212 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 ASN L 82 GLN H 31 ASN A 107 ASN A 221 GLN B 516 HIS B 595 GLN O 40 GLN O 82 GLN O 92 GLN U 37 GLN U 40 GLN U 55 ASN U 82 GLN D 595 GLN F 516 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 62 GLN C 107 ASN E 62 GLN E 107 ASN P 31 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12519 Z= 0.191 Angle : 0.664 13.674 17007 Z= 0.344 Chirality : 0.045 0.183 1851 Planarity : 0.005 0.043 2214 Dihedral : 5.530 49.211 1862 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.21 % Allowed : 14.56 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.19), residues: 1554 helix: 1.29 (0.44), residues: 144 sheet: 0.34 (0.20), residues: 576 loop : -0.90 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 47 HIS 0.007 0.001 HIS A 39 PHE 0.014 0.001 PHE E 225 TYR 0.013 0.001 TYR Y 82 ARG 0.005 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 228 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8070 (pttt) cc_final: 0.7829 (pttm) REVERT: H 56 ASP cc_start: 0.8286 (m-30) cc_final: 0.7919 (m-30) REVERT: H 91 GLU cc_start: 0.6898 (pm20) cc_final: 0.6538 (pm20) REVERT: A 140 LYS cc_start: 0.8370 (tttt) cc_final: 0.7960 (mtpp) REVERT: A 216 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7561 (p) REVERT: B 587 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7511 (ttm110) REVERT: U 48 LYS cc_start: 0.8156 (pttt) cc_final: 0.7947 (pttm) REVERT: D 587 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7372 (ttm110) REVERT: F 587 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7119 (ttt180) REVERT: C 84 LYS cc_start: 0.8612 (mttt) cc_final: 0.8406 (mtpt) REVERT: C 106 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7580 (tp30) REVERT: C 112 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: C 150 ASP cc_start: 0.7067 (m-30) cc_final: 0.6823 (m-30) REVERT: C 216 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8305 (p) REVERT: E 140 LYS cc_start: 0.8391 (tttt) cc_final: 0.8119 (mtpp) REVERT: P 43 LYS cc_start: 0.8095 (mppt) cc_final: 0.7677 (mmtm) REVERT: P 91 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6570 (pm20) REVERT: Y 43 LYS cc_start: 0.7649 (mppt) cc_final: 0.7387 (mmtm) outliers start: 54 outliers final: 27 residues processed: 261 average time/residue: 1.3011 time to fit residues: 367.9522 Evaluate side-chains 238 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.1980 chunk 43 optimal weight: 0.4980 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 ASN H 31 ASN A 62 GLN B 586 ASN O 82 GLN D 567 GLN D 586 ASN D 595 GLN F 586 ASN F 595 GLN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN Y 31 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12519 Z= 0.191 Angle : 0.627 13.427 17007 Z= 0.320 Chirality : 0.044 0.141 1851 Planarity : 0.004 0.030 2214 Dihedral : 5.028 31.981 1854 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.75 % Allowed : 16.28 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.20), residues: 1554 helix: 1.22 (0.44), residues: 144 sheet: 0.43 (0.19), residues: 591 loop : -0.84 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 114 HIS 0.002 0.001 HIS A 39 PHE 0.013 0.001 PHE H 70 TYR 0.013 0.002 TYR E 137 ARG 0.006 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 203 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8129 (pttt) cc_final: 0.7879 (pttm) REVERT: H 89 ARG cc_start: 0.7515 (ptp90) cc_final: 0.7288 (ptp90) REVERT: A 112 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: A 140 LYS cc_start: 0.8428 (tttt) cc_final: 0.8010 (mtpp) REVERT: A 216 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7577 (p) REVERT: B 587 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7481 (ttm110) REVERT: U 48 LYS cc_start: 0.8199 (pttt) cc_final: 0.7984 (pttm) REVERT: U 57 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8306 (mtm180) REVERT: D 587 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7349 (ttm110) REVERT: F 587 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7137 (ttt180) REVERT: C 84 LYS cc_start: 0.8672 (mttt) cc_final: 0.8466 (mtpt) REVERT: C 106 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7539 (tp30) REVERT: E 71 GLU cc_start: 0.7234 (tt0) cc_final: 0.7006 (pt0) REVERT: E 140 LYS cc_start: 0.8415 (tttt) cc_final: 0.8111 (mtpp) REVERT: P 43 LYS cc_start: 0.8037 (mppt) cc_final: 0.7767 (mppt) REVERT: P 91 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6572 (pm20) REVERT: Y 43 LYS cc_start: 0.7660 (mppt) cc_final: 0.7401 (mppt) REVERT: Y 91 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6823 (pm20) outliers start: 61 outliers final: 34 residues processed: 242 average time/residue: 1.3257 time to fit residues: 346.6892 Evaluate side-chains 233 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN A 62 GLN B 595 GLN D 595 GLN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12519 Z= 0.367 Angle : 0.731 12.629 17007 Z= 0.377 Chirality : 0.049 0.155 1851 Planarity : 0.005 0.041 2214 Dihedral : 5.288 30.263 1852 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 6.15 % Allowed : 15.50 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.19), residues: 1554 helix: 1.41 (0.43), residues: 126 sheet: 0.13 (0.20), residues: 576 loop : -0.89 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 PHE 0.017 0.002 PHE P 70 TYR 0.016 0.003 TYR P 97 ARG 0.006 0.001 ARG Y 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 197 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8290 (pttt) cc_final: 0.8054 (pttm) REVERT: A 112 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: A 140 LYS cc_start: 0.8524 (tttt) cc_final: 0.8139 (mtpp) REVERT: A 216 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7657 (p) REVERT: B 587 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7531 (ttm110) REVERT: U 48 LYS cc_start: 0.8334 (pttt) cc_final: 0.8103 (pttm) REVERT: D 564 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6977 (mt-10) REVERT: D 587 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7317 (ttm110) REVERT: F 548 MET cc_start: 0.8271 (mtm) cc_final: 0.8038 (mtp) REVERT: F 587 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7186 (mtp85) REVERT: F 595 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.5767 (mp10) REVERT: C 84 LYS cc_start: 0.8766 (mttt) cc_final: 0.8538 (mtpt) REVERT: C 112 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: C 156 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: E 112 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: E 140 LYS cc_start: 0.8493 (tttt) cc_final: 0.8130 (mtpp) REVERT: E 156 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: P 43 LYS cc_start: 0.8109 (mppt) cc_final: 0.7718 (mppt) REVERT: P 91 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6856 (pm20) REVERT: Y 43 LYS cc_start: 0.7804 (mppt) cc_final: 0.7461 (mppt) REVERT: Y 89 ARG cc_start: 0.7630 (ptp-170) cc_final: 0.7419 (ptp90) REVERT: Y 91 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6906 (pm20) outliers start: 79 outliers final: 51 residues processed: 245 average time/residue: 1.2721 time to fit residues: 337.9164 Evaluate side-chains 254 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 196 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN U 37 GLN D 595 GLN F 586 ASN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Y 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12519 Z= 0.188 Angle : 0.598 12.199 17007 Z= 0.307 Chirality : 0.044 0.135 1851 Planarity : 0.004 0.037 2214 Dihedral : 4.919 26.926 1852 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.37 % Allowed : 16.28 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.20), residues: 1554 helix: 1.61 (0.43), residues: 126 sheet: 0.11 (0.20), residues: 567 loop : -0.79 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 47 HIS 0.002 0.001 HIS C 154 PHE 0.012 0.001 PHE C 225 TYR 0.010 0.001 TYR E 137 ARG 0.005 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 199 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8240 (pttt) cc_final: 0.8014 (pttm) REVERT: A 112 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: A 140 LYS cc_start: 0.8465 (tttt) cc_final: 0.8068 (mtpp) REVERT: A 216 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7710 (p) REVERT: B 587 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7509 (ttm110) REVERT: O 97 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7844 (mtm-85) REVERT: O 112 VAL cc_start: 0.7303 (m) cc_final: 0.7097 (m) REVERT: U 48 LYS cc_start: 0.8277 (pttt) cc_final: 0.8037 (pttm) REVERT: D 587 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7312 (ttm110) REVERT: F 548 MET cc_start: 0.8206 (mtm) cc_final: 0.8002 (mtp) REVERT: F 587 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7145 (ttt90) REVERT: F 595 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.5721 (mp10) REVERT: C 84 LYS cc_start: 0.8719 (mttt) cc_final: 0.8512 (mtpt) REVERT: C 112 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: E 140 LYS cc_start: 0.8452 (tttt) cc_final: 0.8106 (mtpp) REVERT: P 43 LYS cc_start: 0.8030 (mppt) cc_final: 0.7689 (mppt) REVERT: Y 43 LYS cc_start: 0.7707 (mppt) cc_final: 0.7494 (mppt) REVERT: Y 89 ARG cc_start: 0.7818 (ptp-170) cc_final: 0.7557 (ptp90) REVERT: Y 91 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6964 (pm20) outliers start: 69 outliers final: 37 residues processed: 243 average time/residue: 1.3539 time to fit residues: 354.6638 Evaluate side-chains 236 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN D 595 GLN F 586 ASN ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Y 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12519 Z= 0.352 Angle : 0.688 12.101 17007 Z= 0.355 Chirality : 0.047 0.150 1851 Planarity : 0.005 0.043 2214 Dihedral : 5.164 28.508 1852 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.98 % Allowed : 17.06 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1554 helix: 1.22 (0.42), residues: 126 sheet: 0.01 (0.20), residues: 567 loop : -0.86 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 PHE 0.014 0.002 PHE Y 70 TYR 0.014 0.002 TYR Y 97 ARG 0.009 0.001 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 198 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8298 (pttt) cc_final: 0.8058 (pttm) REVERT: A 112 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: A 140 LYS cc_start: 0.8529 (tttt) cc_final: 0.8138 (mtpp) REVERT: B 587 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7528 (ttm110) REVERT: O 112 VAL cc_start: 0.7283 (m) cc_final: 0.7083 (m) REVERT: U 48 LYS cc_start: 0.8358 (pttt) cc_final: 0.8120 (pttm) REVERT: D 587 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7316 (ttm110) REVERT: F 548 MET cc_start: 0.8292 (mtm) cc_final: 0.8089 (mtp) REVERT: F 587 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7188 (mtp85) REVERT: F 595 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.5669 (mp10) REVERT: C 84 LYS cc_start: 0.8753 (mttt) cc_final: 0.8532 (mtpt) REVERT: C 112 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: E 112 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: E 140 LYS cc_start: 0.8463 (tttt) cc_final: 0.8103 (mtpp) REVERT: P 43 LYS cc_start: 0.8034 (mppt) cc_final: 0.7829 (mppt) REVERT: Y 91 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6958 (pm20) outliers start: 64 outliers final: 46 residues processed: 234 average time/residue: 1.4209 time to fit residues: 358.7531 Evaluate side-chains 243 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 193 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN D 595 GLN F 586 ASN ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Y 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12519 Z= 0.227 Angle : 0.608 12.102 17007 Z= 0.313 Chirality : 0.044 0.148 1851 Planarity : 0.004 0.040 2214 Dihedral : 4.935 27.760 1851 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.36 % Allowed : 17.99 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.20), residues: 1554 helix: 1.35 (0.42), residues: 126 sheet: -0.05 (0.20), residues: 567 loop : -0.75 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 47 HIS 0.002 0.001 HIS C 154 PHE 0.014 0.001 PHE F 582 TYR 0.011 0.002 TYR E 137 ARG 0.009 0.001 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 195 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8274 (pttt) cc_final: 0.8032 (pttm) REVERT: L 88 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7313 (t0) REVERT: A 112 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: A 140 LYS cc_start: 0.8479 (tttt) cc_final: 0.8092 (mtpp) REVERT: B 587 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7500 (ttm110) REVERT: U 48 LYS cc_start: 0.8336 (pttt) cc_final: 0.8093 (pttm) REVERT: D 587 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7303 (ttm110) REVERT: F 587 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7172 (mtp85) REVERT: F 595 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.5688 (mp10) REVERT: C 84 LYS cc_start: 0.8754 (mttt) cc_final: 0.8530 (mtmt) REVERT: C 112 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: E 140 LYS cc_start: 0.8453 (tttt) cc_final: 0.8113 (mtpp) REVERT: P 91 GLU cc_start: 0.7142 (pm20) cc_final: 0.6594 (pm20) outliers start: 56 outliers final: 40 residues processed: 229 average time/residue: 1.3686 time to fit residues: 337.9087 Evaluate side-chains 235 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 191 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN U 37 GLN D 595 GLN F 586 ASN ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12519 Z= 0.296 Angle : 0.656 11.699 17007 Z= 0.338 Chirality : 0.046 0.143 1851 Planarity : 0.005 0.046 2214 Dihedral : 5.060 28.121 1851 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.44 % Allowed : 18.38 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.20), residues: 1554 helix: 1.26 (0.42), residues: 126 sheet: -0.11 (0.20), residues: 567 loop : -0.80 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 PHE 0.013 0.002 PHE F 582 TYR 0.014 0.002 TYR Y 97 ARG 0.010 0.001 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 191 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 88 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7324 (t0) REVERT: H 89 ARG cc_start: 0.7846 (ptp90) cc_final: 0.7280 (ptp90) REVERT: A 112 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: A 140 LYS cc_start: 0.8498 (tttt) cc_final: 0.8116 (mtpp) REVERT: B 587 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7488 (ttm110) REVERT: U 48 LYS cc_start: 0.8358 (pttt) cc_final: 0.8114 (pttm) REVERT: D 587 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7284 (ttm110) REVERT: F 587 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7148 (ttt180) REVERT: F 595 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.5698 (mp10) REVERT: C 84 LYS cc_start: 0.8763 (mttt) cc_final: 0.8537 (mtmt) REVERT: C 112 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: E 112 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: E 140 LYS cc_start: 0.8456 (tttt) cc_final: 0.8084 (mtpp) REVERT: P 91 GLU cc_start: 0.7296 (pm20) cc_final: 0.6806 (pm20) REVERT: P 112 ASP cc_start: 0.8076 (m-30) cc_final: 0.7855 (m-30) REVERT: Y 91 GLU cc_start: 0.7442 (pm20) cc_final: 0.7124 (pm20) outliers start: 57 outliers final: 47 residues processed: 223 average time/residue: 1.3527 time to fit residues: 325.4748 Evaluate side-chains 242 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 190 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 40.0000 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN F 586 ASN ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12519 Z= 0.366 Angle : 0.702 11.372 17007 Z= 0.362 Chirality : 0.048 0.162 1851 Planarity : 0.005 0.046 2214 Dihedral : 5.271 29.402 1851 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.52 % Allowed : 18.38 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.19), residues: 1554 helix: 1.04 (0.42), residues: 126 sheet: -0.18 (0.20), residues: 567 loop : -0.99 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 47 HIS 0.004 0.001 HIS C 154 PHE 0.016 0.002 PHE Y 70 TYR 0.016 0.002 TYR Y 97 ARG 0.009 0.001 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 195 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 88 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7336 (t0) REVERT: H 89 ARG cc_start: 0.7949 (ptp90) cc_final: 0.7341 (ptp90) REVERT: A 112 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: A 140 LYS cc_start: 0.8511 (tttt) cc_final: 0.8128 (mtpp) REVERT: B 587 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7488 (ttm110) REVERT: D 587 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7273 (ttm110) REVERT: F 587 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7187 (ttt180) REVERT: F 595 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.5732 (mp10) REVERT: C 84 LYS cc_start: 0.8774 (mttt) cc_final: 0.8528 (mtpt) REVERT: C 112 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: E 112 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7837 (mt-10) REVERT: E 140 LYS cc_start: 0.8442 (tttt) cc_final: 0.8097 (mtpp) REVERT: P 61 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6735 (m-30) REVERT: P 91 GLU cc_start: 0.7371 (pm20) cc_final: 0.6857 (pm20) REVERT: Y 48 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7721 (p) REVERT: Y 91 GLU cc_start: 0.7589 (pm20) cc_final: 0.7238 (pm20) outliers start: 58 outliers final: 48 residues processed: 228 average time/residue: 1.4078 time to fit residues: 345.5228 Evaluate side-chains 244 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 189 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 95 optimal weight: 0.0970 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12519 Z= 0.156 Angle : 0.561 11.237 17007 Z= 0.288 Chirality : 0.043 0.158 1851 Planarity : 0.004 0.038 2214 Dihedral : 4.808 27.378 1851 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.96 % Allowed : 20.33 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.20), residues: 1554 helix: 0.80 (0.41), residues: 144 sheet: -0.07 (0.21), residues: 555 loop : -0.73 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 47 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE F 582 TYR 0.013 0.001 TYR F 517 ARG 0.008 0.000 ARG B 596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 203 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 88 ASP cc_start: 0.7555 (m-30) cc_final: 0.7310 (t0) REVERT: A 140 LYS cc_start: 0.8424 (tttt) cc_final: 0.8035 (mtpp) REVERT: B 587 ARG cc_start: 0.7772 (mtt180) cc_final: 0.7240 (ttt180) REVERT: U 48 LYS cc_start: 0.8316 (pttp) cc_final: 0.8036 (pttm) REVERT: D 587 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7268 (ttm110) REVERT: F 587 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7135 (ttt180) REVERT: F 595 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.5769 (mp10) REVERT: C 84 LYS cc_start: 0.8741 (mttt) cc_final: 0.8527 (mtmt) REVERT: E 140 LYS cc_start: 0.8425 (tttt) cc_final: 0.8077 (mtpp) REVERT: P 91 GLU cc_start: 0.7352 (pm20) cc_final: 0.6814 (pm20) REVERT: P 112 ASP cc_start: 0.8003 (m-30) cc_final: 0.7799 (m-30) REVERT: Y 91 GLU cc_start: 0.7580 (pm20) cc_final: 0.7237 (pm20) outliers start: 38 outliers final: 30 residues processed: 227 average time/residue: 1.3173 time to fit residues: 323.1298 Evaluate side-chains 228 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 105 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN D 567 GLN D 595 GLN F 586 ASN ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.173692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136711 restraints weight = 13487.891| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.11 r_work: 0.3177 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12519 Z= 0.307 Angle : 0.655 11.198 17007 Z= 0.337 Chirality : 0.046 0.166 1851 Planarity : 0.005 0.045 2214 Dihedral : 5.050 28.265 1851 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.35 % Allowed : 19.94 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.20), residues: 1554 helix: 1.33 (0.42), residues: 126 sheet: -0.09 (0.21), residues: 567 loop : -0.82 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 PHE 0.012 0.002 PHE Y 70 TYR 0.014 0.002 TYR F 517 ARG 0.010 0.001 ARG B 596 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5374.94 seconds wall clock time: 95 minutes 40.89 seconds (5740.89 seconds total)