Starting phenix.real_space_refine on Tue Jun 17 01:23:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qer_13938/06_2025/7qer_13938.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qer_13938/06_2025/7qer_13938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qer_13938/06_2025/7qer_13938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qer_13938/06_2025/7qer_13938.map" model { file = "/net/cci-nas-00/data/ceres_data/7qer_13938/06_2025/7qer_13938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qer_13938/06_2025/7qer_13938.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 168 5.16 5 C 12648 2.51 5 N 2928 2.21 5 O 3353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19097 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "B" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "C" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "D" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "E" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "F" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "G" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "I" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "J" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "K" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "L" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} 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: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 11.54, per 1000 atoms: 0.60 Number of scatterers: 19097 At special positions: 0 Unit cell: (101.37, 111.18, 153.69, 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 168 16.00 O 3353 8.00 N 2928 7.00 C 12648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.04 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.04 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.04 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.04 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.04 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.04 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.04 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.04 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.04 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.04 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.04 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.04 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.04 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.04 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.04 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.04 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.04 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.04 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.04 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.04 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.04 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.14 Conformation dependent library (CDL) restraints added in 2.1 seconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 4.340A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 101 Proline residue: A 87 - end of helix removed outlier: 3.566A pdb=" N VAL A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 217 Processing helix chain 'B' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.340A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 101 Proline residue: B 87 - end of helix removed outlier: 3.566A pdb=" N VAL B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 217 Processing helix chain 'C' and resid 5 through 15 removed outlier: 4.258A pdb=" N ILE C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 39 removed outlier: 4.339A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 43 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 101 Proline residue: C 87 - end of helix removed outlier: 3.566A pdb=" N VAL C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 144 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 217 Processing helix chain 'D' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 39 removed outlier: 4.341A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 43 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 101 Proline residue: D 87 - end of helix removed outlier: 3.567A pdb=" N VAL D 91 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 217 Processing helix chain 'E' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS E 15 " --> pdb=" O GLY E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 39 removed outlier: 4.340A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 43 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 101 Proline residue: E 87 - end of helix removed outlier: 3.566A pdb=" N VAL E 91 " --> pdb=" O PRO E 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU E 101 " --> pdb=" O TYR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 217 Processing helix chain 'F' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 39 removed outlier: 4.340A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 43 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 101 Proline residue: F 87 - end of helix removed outlier: 3.566A pdb=" N VAL F 91 " --> pdb=" O PRO F 87 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU F 101 " --> pdb=" O TYR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 144 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 217 Processing helix chain 'G' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 39 removed outlier: 4.340A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 43 Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 101 Proline residue: G 87 - end of helix removed outlier: 3.566A pdb=" N VAL G 91 " --> pdb=" O PRO G 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU G 101 " --> pdb=" O TYR G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG G 143 " --> pdb=" O SER G 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 217 Processing helix chain 'H' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE H 9 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 39 removed outlier: 4.340A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 43 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 101 Proline residue: H 87 - end of helix removed outlier: 3.567A pdb=" N VAL H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU H 101 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG H 143 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 217 Processing helix chain 'I' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 39 removed outlier: 4.340A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 43 Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 101 Proline residue: I 87 - end of helix removed outlier: 3.566A pdb=" N VAL I 91 " --> pdb=" O PRO I 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA I 92 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU I 101 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG I 143 " --> pdb=" O SER I 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL I 144 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 217 Processing helix chain 'J' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 39 removed outlier: 4.339A pdb=" N LEU J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 43 Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 101 Proline residue: J 87 - end of helix removed outlier: 3.567A pdb=" N VAL J 91 " --> pdb=" O PRO J 87 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA J 92 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU J 101 " --> pdb=" O TYR J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 159 removed outlier: 3.559A pdb=" N ARG J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL J 144 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 217 Processing helix chain 'K' and resid 5 through 15 removed outlier: 4.259A pdb=" N ILE K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 39 removed outlier: 4.339A pdb=" N LEU K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 43 Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 101 Proline residue: K 87 - end of helix removed outlier: 3.567A pdb=" N VAL K 91 " --> pdb=" O PRO K 87 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU K 101 " --> pdb=" O TYR K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG K 143 " --> pdb=" O SER K 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL K 144 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 217 Processing helix chain 'L' and resid 5 through 15 removed outlier: 4.258A pdb=" N ILE L 9 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 39 removed outlier: 4.340A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 43 Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 101 Proline residue: L 87 - end of helix removed outlier: 3.566A pdb=" N VAL L 91 " --> pdb=" O PRO L 87 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU L 101 " --> pdb=" O TYR L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 159 removed outlier: 3.560A pdb=" N ARG L 143 " --> pdb=" O SER L 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL L 144 " --> pdb=" O ILE L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 1308 hydrogen bonds defined for protein. 3816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5399 1.34 - 1.46: 3886 1.46 - 1.57: 9723 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 19248 Sorted by residual: bond pdb=" C1 LMT B 303 " pdb=" C2 LMT B 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" C1 LMT H 305 " pdb=" C2 LMT H 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C1 LMT D 303 " pdb=" C2 LMT D 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 LMT F 301 " pdb=" C2 LMT F 301 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 LMT D 305 " pdb=" C2 LMT D 305 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.00e-02 2.50e+03 5.86e+00 ... (remaining 19243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 24970 1.61 - 3.21: 530 3.21 - 4.82: 154 4.82 - 6.43: 179 6.43 - 8.03: 123 Bond angle restraints: 25956 Sorted by residual: angle pdb=" C2 LMT C 301 " pdb=" C3 LMT C 301 " pdb=" C4 LMT C 301 " ideal model delta sigma weight residual 117.09 109.06 8.03 3.00e+00 1.11e-01 7.17e+00 angle pdb=" C2 LMT L 304 " pdb=" C3 LMT L 304 " pdb=" C4 LMT L 304 " ideal model delta sigma weight residual 117.09 109.06 8.03 3.00e+00 1.11e-01 7.17e+00 angle pdb=" C2 LMT E 301 " pdb=" C3 LMT E 301 " pdb=" C4 LMT E 301 " ideal model delta sigma weight residual 117.09 109.07 8.02 3.00e+00 1.11e-01 7.15e+00 angle pdb=" C2 LMT D 301 " pdb=" C3 LMT D 301 " pdb=" C4 LMT D 301 " ideal model delta sigma weight residual 117.09 109.07 8.02 3.00e+00 1.11e-01 7.14e+00 angle pdb=" C2 LMT H 301 " pdb=" C3 LMT H 301 " pdb=" C4 LMT H 301 " ideal model delta sigma weight residual 117.09 109.08 8.01 3.00e+00 1.11e-01 7.14e+00 ... (remaining 25951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.97: 9602 11.97 - 23.93: 1006 23.93 - 35.89: 233 35.89 - 47.86: 220 47.86 - 59.82: 123 Dihedral angle restraints: 11184 sinusoidal: 4584 harmonic: 6600 Sorted by residual: dihedral pdb=" CA ALA B 39 " pdb=" C ALA B 39 " pdb=" N ALA B 40 " pdb=" CA ALA B 40 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ALA I 39 " pdb=" C ALA I 39 " pdb=" N ALA I 40 " pdb=" CA ALA I 40 " ideal model delta harmonic sigma weight residual 180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ALA A 39 " pdb=" C ALA A 39 " pdb=" N ALA A 40 " pdb=" CA ALA A 40 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1258 0.029 - 0.059: 1193 0.059 - 0.088: 325 0.088 - 0.117: 104 0.117 - 0.147: 48 Chirality restraints: 2928 Sorted by residual: chirality pdb=" CA PRO H 185 " pdb=" N PRO H 185 " pdb=" C PRO H 185 " pdb=" CB PRO H 185 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA PRO J 185 " pdb=" N PRO J 185 " pdb=" C PRO J 185 " pdb=" CB PRO J 185 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA PRO K 185 " pdb=" N PRO K 185 " pdb=" C PRO K 185 " pdb=" CB PRO K 185 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 2925 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 51 " -0.012 2.00e-02 2.50e+03 9.03e-03 1.43e+00 pdb=" CG PHE G 51 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE G 51 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE G 51 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE G 51 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE G 51 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 51 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 51 " -0.012 2.00e-02 2.50e+03 9.00e-03 1.42e+00 pdb=" CG PHE I 51 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE I 51 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 51 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE I 51 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE I 51 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE I 51 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 51 " 0.012 2.00e-02 2.50e+03 8.98e-03 1.41e+00 pdb=" CG PHE F 51 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE F 51 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 51 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 51 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 51 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 51 " 0.003 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 264 2.67 - 3.23: 18117 3.23 - 3.79: 28827 3.79 - 4.34: 39094 4.34 - 4.90: 63604 Nonbonded interactions: 149906 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.117 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.117 3.040 nonbonded pdb=" O ILE K 71 " pdb=" OH TYR K 158 " model vdw 2.117 3.040 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.117 3.040 nonbonded pdb=" O ILE E 71 " pdb=" OH TYR E 158 " model vdw 2.117 3.040 ... (remaining 149901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'B' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'C' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'D' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'E' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'F' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) selection = (chain 'G' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'H' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'I' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'J' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'K' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'L' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } 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: 2.690 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 39.940 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 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 : 0.009 0.049 19284 Z= 0.384 Angle : 0.942 8.035 26028 Z= 0.414 Chirality : 0.046 0.147 2928 Planarity : 0.003 0.023 3072 Dihedral : 14.111 59.824 6804 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.94 % Allowed : 10.23 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.05 (0.17), residues: 2196 helix: 0.38 (0.13), residues: 1524 sheet: 1.59 (0.40), residues: 132 loop : -1.42 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 172 HIS 0.003 0.001 HIS J 73 PHE 0.020 0.002 PHE F 51 TYR 0.016 0.002 TYR F 65 ARG 0.002 0.000 ARG L 165 Details of bonding type rmsd hydrogen bonds : bond 0.24705 ( 1308) hydrogen bonds : angle 7.22735 ( 3816) SS BOND : bond 0.00598 ( 36) SS BOND : angle 1.93578 ( 72) covalent geometry : bond 0.00867 (19248) covalent geometry : angle 0.93816 (25956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 97 TYR cc_start: 0.7499 (t80) cc_final: 0.7070 (t80) REVERT: E 136 TYR cc_start: 0.7703 (t80) cc_final: 0.7484 (t80) REVERT: E 209 GLU cc_start: 0.8677 (tt0) cc_final: 0.8407 (tt0) REVERT: I 97 TYR cc_start: 0.7511 (t80) cc_final: 0.6658 (t80) REVERT: J 97 TYR cc_start: 0.7647 (t80) cc_final: 0.7108 (t80) REVERT: J 140 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8657 (mp) REVERT: K 22 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7729 (ttmm) REVERT: K 134 TRP cc_start: 0.7925 (m100) cc_final: 0.7682 (m-10) REVERT: K 140 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8555 (mp) REVERT: K 214 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8237 (tp) outliers start: 59 outliers final: 16 residues processed: 319 average time/residue: 1.3300 time to fit residues: 476.6245 Evaluate side-chains 244 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 0.0870 chunk 126 optimal weight: 0.4980 chunk 196 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN C 57 GLN E 57 GLN E 206 ASN F 57 GLN G 57 GLN I 57 GLN L 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.128253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.078751 restraints weight = 28555.339| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.88 r_work: 0.2881 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19284 Z= 0.166 Angle : 0.623 8.927 26028 Z= 0.331 Chirality : 0.044 0.166 2928 Planarity : 0.004 0.024 3072 Dihedral : 10.939 59.387 2813 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.30 % Allowed : 15.02 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.18), residues: 2196 helix: 2.19 (0.13), residues: 1572 sheet: 2.03 (0.39), residues: 132 loop : -1.46 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 133 HIS 0.002 0.001 HIS G 73 PHE 0.012 0.002 PHE D 31 TYR 0.011 0.002 TYR A 65 ARG 0.008 0.000 ARG K 216 Details of bonding type rmsd hydrogen bonds : bond 0.07809 ( 1308) hydrogen bonds : angle 4.15805 ( 3816) SS BOND : bond 0.00179 ( 36) SS BOND : angle 1.02463 ( 72) covalent geometry : bond 0.00303 (19248) covalent geometry : angle 0.62114 (25956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7721 (mp) REVERT: C 97 TYR cc_start: 0.7736 (t80) cc_final: 0.7282 (t80) REVERT: C 143 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7890 (mtt90) REVERT: E 136 TYR cc_start: 0.7254 (t80) cc_final: 0.7026 (t80) REVERT: E 216 ARG cc_start: 0.7413 (tmm-80) cc_final: 0.7196 (tmm-80) REVERT: F 216 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7892 (tmm-80) REVERT: G 216 ARG cc_start: 0.7921 (tmm-80) cc_final: 0.7714 (tmm-80) REVERT: H 93 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7770 (mtt) REVERT: I 97 TYR cc_start: 0.7748 (t80) cc_final: 0.7491 (t80) REVERT: J 22 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7739 (tppp) REVERT: J 97 TYR cc_start: 0.7553 (t80) cc_final: 0.7005 (t80) REVERT: K 22 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7749 (tppt) REVERT: K 134 TRP cc_start: 0.8136 (m100) cc_final: 0.7851 (m-10) REVERT: L 140 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7946 (mp) outliers start: 26 outliers final: 9 residues processed: 290 average time/residue: 1.5282 time to fit residues: 494.1683 Evaluate side-chains 267 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 254 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 162 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN C 94 HIS E 57 GLN E 206 ASN F 57 GLN G 57 GLN I 57 GLN L 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.127484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.076997 restraints weight = 28210.087| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.89 r_work: 0.2838 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19284 Z= 0.150 Angle : 0.569 7.077 26028 Z= 0.308 Chirality : 0.044 0.183 2928 Planarity : 0.003 0.029 3072 Dihedral : 9.646 59.763 2796 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.20 % Allowed : 15.52 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.18), residues: 2196 helix: 2.71 (0.13), residues: 1596 sheet: 2.34 (0.41), residues: 132 loop : -1.53 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 133 HIS 0.005 0.001 HIS C 94 PHE 0.015 0.002 PHE H 51 TYR 0.017 0.002 TYR L 212 ARG 0.007 0.000 ARG K 216 Details of bonding type rmsd hydrogen bonds : bond 0.06769 ( 1308) hydrogen bonds : angle 3.87062 ( 3816) SS BOND : bond 0.00296 ( 36) SS BOND : angle 1.06323 ( 72) covalent geometry : bond 0.00322 (19248) covalent geometry : angle 0.56717 (25956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6439 (t80) REVERT: B 212 TYR cc_start: 0.7346 (m-80) cc_final: 0.7092 (m-10) REVERT: C 97 TYR cc_start: 0.7508 (t80) cc_final: 0.7025 (t80) REVERT: E 136 TYR cc_start: 0.7467 (t80) cc_final: 0.7133 (t80) REVERT: E 216 ARG cc_start: 0.7362 (tmm-80) cc_final: 0.7155 (tmm-80) REVERT: I 97 TYR cc_start: 0.7867 (t80) cc_final: 0.7605 (t80) REVERT: J 22 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7748 (tppp) REVERT: J 97 TYR cc_start: 0.7600 (t80) cc_final: 0.7033 (t80) REVERT: K 22 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7872 (ttmm) REVERT: K 134 TRP cc_start: 0.8189 (m100) cc_final: 0.7863 (m-10) outliers start: 44 outliers final: 21 residues processed: 292 average time/residue: 1.3705 time to fit residues: 448.2483 Evaluate side-chains 278 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 155 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS K 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.124752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.073457 restraints weight = 28313.482| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.87 r_work: 0.2765 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 19284 Z= 0.254 Angle : 0.665 7.990 26028 Z= 0.364 Chirality : 0.049 0.176 2928 Planarity : 0.004 0.037 3072 Dihedral : 9.891 58.823 2784 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.89 % Allowed : 17.02 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.18), residues: 2196 helix: 2.64 (0.13), residues: 1596 sheet: 2.05 (0.42), residues: 132 loop : -1.39 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 172 HIS 0.008 0.001 HIS C 73 PHE 0.019 0.002 PHE K 51 TYR 0.022 0.002 TYR I 68 ARG 0.004 0.001 ARG C 184 Details of bonding type rmsd hydrogen bonds : bond 0.07856 ( 1308) hydrogen bonds : angle 4.12385 ( 3816) SS BOND : bond 0.00593 ( 36) SS BOND : angle 1.60821 ( 72) covalent geometry : bond 0.00609 (19248) covalent geometry : angle 0.66001 (25956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 TYR cc_start: 0.7465 (m-80) cc_final: 0.7166 (m-10) REVERT: C 97 TYR cc_start: 0.7616 (t80) cc_final: 0.7094 (t80) REVERT: D 212 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6718 (t80) REVERT: F 159 ASP cc_start: 0.8710 (p0) cc_final: 0.8263 (p0) REVERT: F 212 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6696 (t80) REVERT: H 212 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6582 (t80) REVERT: J 22 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7827 (ttmm) REVERT: L 212 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6438 (t80) outliers start: 58 outliers final: 45 residues processed: 292 average time/residue: 1.3126 time to fit residues: 431.6876 Evaluate side-chains 292 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 163 MET Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 215 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 10 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 185 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.129073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079230 restraints weight = 28198.629| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.84 r_work: 0.2880 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19284 Z= 0.126 Angle : 0.528 8.263 26028 Z= 0.286 Chirality : 0.043 0.166 2928 Planarity : 0.003 0.028 3072 Dihedral : 8.635 57.306 2784 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.09 % Allowed : 16.87 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.18), residues: 2196 helix: 3.10 (0.13), residues: 1596 sheet: 2.32 (0.43), residues: 132 loop : -1.60 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 133 HIS 0.004 0.000 HIS C 94 PHE 0.009 0.001 PHE I 31 TYR 0.009 0.001 TYR G 158 ARG 0.002 0.000 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 1308) hydrogen bonds : angle 3.69351 ( 3816) SS BOND : bond 0.00205 ( 36) SS BOND : angle 0.87622 ( 72) covalent geometry : bond 0.00253 (19248) covalent geometry : angle 0.52701 (25956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 257 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6542 (t80) REVERT: B 212 TYR cc_start: 0.7367 (m-80) cc_final: 0.6882 (t80) REVERT: C 97 TYR cc_start: 0.7622 (t80) cc_final: 0.7067 (t80) REVERT: D 212 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6790 (t80) REVERT: F 212 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6689 (t80) REVERT: G 159 ASP cc_start: 0.8596 (p0) cc_final: 0.8118 (p0) REVERT: H 212 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6793 (t80) REVERT: J 22 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7638 (tppp) REVERT: L 212 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.6367 (t80) outliers start: 62 outliers final: 33 residues processed: 296 average time/residue: 1.3011 time to fit residues: 433.7679 Evaluate side-chains 284 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 211 CYS Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 215 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 176 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 211 optimal weight: 0.0470 chunk 28 optimal weight: 7.9990 chunk 144 optimal weight: 0.0170 chunk 116 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.127402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076247 restraints weight = 28196.566| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.87 r_work: 0.2825 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19284 Z= 0.153 Angle : 0.572 9.410 26028 Z= 0.310 Chirality : 0.044 0.175 2928 Planarity : 0.003 0.031 3072 Dihedral : 8.255 59.865 2784 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.54 % Allowed : 18.01 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.18), residues: 2196 helix: 3.13 (0.13), residues: 1596 sheet: 2.27 (0.42), residues: 132 loop : -1.55 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 133 HIS 0.005 0.001 HIS C 94 PHE 0.013 0.002 PHE K 51 TYR 0.016 0.002 TYR K 65 ARG 0.007 0.000 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.06230 ( 1308) hydrogen bonds : angle 3.76005 ( 3816) SS BOND : bond 0.00342 ( 36) SS BOND : angle 1.10340 ( 72) covalent geometry : bond 0.00346 (19248) covalent geometry : angle 0.56957 (25956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 TYR cc_start: 0.7392 (m-80) cc_final: 0.6937 (t80) REVERT: B 217 TYR cc_start: 0.6182 (OUTLIER) cc_final: 0.5806 (t80) REVERT: D 212 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6806 (t80) REVERT: F 159 ASP cc_start: 0.8723 (p0) cc_final: 0.8386 (p0) REVERT: F 212 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6733 (t80) REVERT: G 8 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7417 (p) REVERT: G 159 ASP cc_start: 0.8736 (p0) cc_final: 0.8339 (p0) REVERT: H 212 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6756 (t80) REVERT: L 212 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6388 (t80) outliers start: 51 outliers final: 36 residues processed: 284 average time/residue: 1.3705 time to fit residues: 436.9346 Evaluate side-chains 284 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 215 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 62 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.127303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076130 restraints weight = 28039.805| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.87 r_work: 0.2823 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19284 Z= 0.154 Angle : 0.566 7.997 26028 Z= 0.307 Chirality : 0.044 0.185 2928 Planarity : 0.003 0.031 3072 Dihedral : 7.958 59.010 2784 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.59 % Allowed : 18.36 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.18), residues: 2196 helix: 3.17 (0.13), residues: 1596 sheet: 2.21 (0.42), residues: 132 loop : -1.51 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 133 HIS 0.005 0.001 HIS C 94 PHE 0.013 0.002 PHE K 51 TYR 0.014 0.002 TYR H 65 ARG 0.007 0.000 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.06176 ( 1308) hydrogen bonds : angle 3.75666 ( 3816) SS BOND : bond 0.00351 ( 36) SS BOND : angle 1.11211 ( 72) covalent geometry : bond 0.00351 (19248) covalent geometry : angle 0.56373 (25956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6681 (t80) REVERT: B 212 TYR cc_start: 0.7453 (m-80) cc_final: 0.7026 (t80) REVERT: C 42 GLU cc_start: 0.8312 (tp30) cc_final: 0.7989 (tp30) REVERT: D 212 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6850 (t80) REVERT: F 159 ASP cc_start: 0.8802 (p0) cc_final: 0.8481 (p0) REVERT: F 212 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6659 (t80) REVERT: G 8 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7427 (p) REVERT: G 159 ASP cc_start: 0.8791 (p0) cc_final: 0.8394 (p0) REVERT: H 212 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6739 (t80) REVERT: L 212 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.6381 (t80) outliers start: 52 outliers final: 36 residues processed: 280 average time/residue: 1.3484 time to fit residues: 424.2086 Evaluate side-chains 285 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 211 CYS Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 215 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 166 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.128557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077764 restraints weight = 28239.470| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.87 r_work: 0.2858 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19284 Z= 0.127 Angle : 0.542 9.474 26028 Z= 0.290 Chirality : 0.043 0.180 2928 Planarity : 0.003 0.028 3072 Dihedral : 7.162 59.956 2784 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.64 % Allowed : 18.61 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.18), residues: 2196 helix: 3.31 (0.13), residues: 1596 sheet: 2.27 (0.42), residues: 132 loop : -1.60 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 133 HIS 0.004 0.001 HIS C 94 PHE 0.011 0.001 PHE L 31 TYR 0.010 0.001 TYR C 158 ARG 0.007 0.000 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.05467 ( 1308) hydrogen bonds : angle 3.63127 ( 3816) SS BOND : bond 0.00251 ( 36) SS BOND : angle 0.92313 ( 72) covalent geometry : bond 0.00271 (19248) covalent geometry : angle 0.54058 (25956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6677 (t80) REVERT: B 212 TYR cc_start: 0.7554 (m-80) cc_final: 0.7105 (t80) REVERT: B 217 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.5684 (t80) REVERT: C 42 GLU cc_start: 0.8375 (tp30) cc_final: 0.8062 (tp30) REVERT: C 99 ARG cc_start: 0.7678 (mmt180) cc_final: 0.7265 (ttp80) REVERT: C 159 ASP cc_start: 0.8692 (p0) cc_final: 0.8220 (p0) REVERT: D 212 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6825 (t80) REVERT: F 159 ASP cc_start: 0.8780 (p0) cc_final: 0.8418 (p0) REVERT: F 212 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6703 (t80) REVERT: G 8 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7422 (p) REVERT: G 159 ASP cc_start: 0.8750 (p0) cc_final: 0.8266 (p0) REVERT: H 42 GLU cc_start: 0.8359 (pt0) cc_final: 0.8120 (pm20) REVERT: H 212 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6784 (t80) REVERT: L 212 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.6311 (t80) outliers start: 53 outliers final: 37 residues processed: 282 average time/residue: 1.3561 time to fit residues: 427.9014 Evaluate side-chains 287 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 211 CYS Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain K residue 163 MET Chi-restraints excluded: chain K residue 211 CYS Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain L residue 215 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 31 optimal weight: 0.0070 chunk 155 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 175 optimal weight: 0.0010 chunk 15 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.129924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079410 restraints weight = 28273.592| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.89 r_work: 0.2893 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19284 Z= 0.116 Angle : 0.522 8.267 26028 Z= 0.279 Chirality : 0.042 0.173 2928 Planarity : 0.003 0.032 3072 Dihedral : 6.139 59.515 2784 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.20 % Allowed : 19.21 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.18), residues: 2196 helix: 3.36 (0.12), residues: 1656 sheet: 2.35 (0.43), residues: 132 loop : -1.36 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 133 HIS 0.005 0.001 HIS C 94 PHE 0.010 0.001 PHE A 31 TYR 0.010 0.001 TYR E 158 ARG 0.007 0.000 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 1308) hydrogen bonds : angle 3.51696 ( 3816) SS BOND : bond 0.00181 ( 36) SS BOND : angle 0.80344 ( 72) covalent geometry : bond 0.00238 (19248) covalent geometry : angle 0.52058 (25956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8257 (pt0) cc_final: 0.8048 (pm20) REVERT: A 212 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6670 (t80) REVERT: B 212 TYR cc_start: 0.7451 (m-80) cc_final: 0.7091 (t80) REVERT: C 42 GLU cc_start: 0.8473 (tp30) cc_final: 0.8091 (tp30) REVERT: C 99 ARG cc_start: 0.7724 (mmt180) cc_final: 0.7279 (ttp80) REVERT: D 42 GLU cc_start: 0.8323 (pt0) cc_final: 0.8098 (pm20) REVERT: D 212 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6769 (t80) REVERT: E 98 ARG cc_start: 0.6620 (tpp-160) cc_final: 0.6320 (tpp80) REVERT: F 159 ASP cc_start: 0.8703 (p0) cc_final: 0.8344 (p0) REVERT: F 212 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6557 (t80) REVERT: G 8 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7421 (p) REVERT: G 159 ASP cc_start: 0.8695 (p0) cc_final: 0.8223 (p0) REVERT: H 42 GLU cc_start: 0.8304 (pt0) cc_final: 0.8066 (pm20) REVERT: H 212 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6722 (t80) REVERT: I 212 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6550 (m-80) REVERT: K 22 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7528 (mmmt) REVERT: L 212 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6385 (t80) outliers start: 44 outliers final: 25 residues processed: 269 average time/residue: 1.3948 time to fit residues: 420.2918 Evaluate side-chains 273 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 177 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.128624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077911 restraints weight = 28089.238| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.86 r_work: 0.2857 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19284 Z= 0.128 Angle : 0.550 10.641 26028 Z= 0.293 Chirality : 0.043 0.182 2928 Planarity : 0.003 0.027 3072 Dihedral : 5.855 59.454 2784 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.80 % Allowed : 19.96 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.18), residues: 2196 helix: 3.34 (0.12), residues: 1656 sheet: 2.33 (0.42), residues: 132 loop : -1.31 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 134 HIS 0.005 0.001 HIS C 94 PHE 0.010 0.001 PHE L 31 TYR 0.012 0.001 TYR A 65 ARG 0.007 0.000 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.05314 ( 1308) hydrogen bonds : angle 3.60053 ( 3816) SS BOND : bond 0.00262 ( 36) SS BOND : angle 0.94056 ( 72) covalent geometry : bond 0.00276 (19248) covalent geometry : angle 0.54833 (25956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6686 (t80) REVERT: B 212 TYR cc_start: 0.7487 (m-80) cc_final: 0.7123 (t80) REVERT: C 42 GLU cc_start: 0.8487 (tp30) cc_final: 0.8119 (tp30) REVERT: C 99 ARG cc_start: 0.7741 (mmt180) cc_final: 0.7301 (ttp80) REVERT: C 159 ASP cc_start: 0.8644 (p0) cc_final: 0.8403 (p0) REVERT: D 212 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6782 (t80) REVERT: E 98 ARG cc_start: 0.6678 (tpp-160) cc_final: 0.6378 (tpp80) REVERT: F 159 ASP cc_start: 0.8713 (p0) cc_final: 0.8263 (p0) REVERT: F 212 TYR cc_start: 0.6969 (OUTLIER) cc_final: 0.6570 (t80) REVERT: G 8 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7425 (p) REVERT: G 159 ASP cc_start: 0.8672 (p0) cc_final: 0.8186 (p0) REVERT: H 212 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6692 (t80) REVERT: I 212 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: L 212 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6482 (t80) outliers start: 36 outliers final: 26 residues processed: 259 average time/residue: 1.3624 time to fit residues: 394.6100 Evaluate side-chains 269 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 217 TYR Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 108 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.127633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.076407 restraints weight = 28223.850| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.86 r_work: 0.2824 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19284 Z= 0.153 Angle : 0.576 8.735 26028 Z= 0.309 Chirality : 0.044 0.191 2928 Planarity : 0.003 0.043 3072 Dihedral : 5.905 58.556 2784 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.85 % Allowed : 19.96 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.18), residues: 2196 helix: 3.36 (0.13), residues: 1596 sheet: 2.25 (0.42), residues: 132 loop : -1.55 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 134 HIS 0.006 0.001 HIS C 94 PHE 0.011 0.002 PHE B 191 TYR 0.016 0.002 TYR A 65 ARG 0.013 0.001 ARG K 216 Details of bonding type rmsd hydrogen bonds : bond 0.05893 ( 1308) hydrogen bonds : angle 3.71286 ( 3816) SS BOND : bond 0.00346 ( 36) SS BOND : angle 1.14360 ( 72) covalent geometry : bond 0.00349 (19248) covalent geometry : angle 0.57343 (25956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23431.00 seconds wall clock time: 402 minutes 25.48 seconds (24145.48 seconds total)