Starting phenix.real_space_refine on Tue Nov 19 11:55:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qer_13938/11_2024/7qer_13938.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qer_13938/11_2024/7qer_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qer_13938/11_2024/7qer_13938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qer_13938/11_2024/7qer_13938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qer_13938/11_2024/7qer_13938.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qer_13938/11_2024/7qer_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 12.33, per 1000 atoms: 0.65 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: 4.67 Conformation dependent library (CDL) restraints added in 2.4 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: 1.72 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: 5.53 Time building geometry restraints manager: 5.31 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: 0.00 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: 3.020 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: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 42.300 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.870 ------------------------------------------------------------------------------- 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 19248 Z= 0.559 Angle : 0.938 8.035 25956 Z= 0.412 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 *********************** 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 : 2.273 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: 1.3060 time to fit residues: 469.0520 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 : 2.047 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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 19248 Z= 0.193 Angle : 0.621 8.925 25956 Z= 0.331 Chirality : 0.044 0.166 2928 Planarity : 0.004 0.024 3072 Dihedral : 10.939 59.386 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 *********************** 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 : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8077 (mtm) cc_final: 0.7845 (mtt) REVERT: B 140 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7963 (mp) REVERT: C 97 TYR cc_start: 0.7583 (t80) cc_final: 0.7145 (t80) REVERT: C 143 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7851 (mtt90) REVERT: D 93 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7993 (mtt) REVERT: H 93 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7701 (mtt) REVERT: I 97 TYR cc_start: 0.7615 (t80) cc_final: 0.7344 (t80) REVERT: J 22 LYS cc_start: 0.8284 (mtpp) cc_final: 0.7777 (tppp) REVERT: J 97 TYR cc_start: 0.7453 (t80) cc_final: 0.6893 (t80) REVERT: K 22 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7743 (tppt) REVERT: L 140 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8222 (mp) outliers start: 26 outliers final: 9 residues processed: 290 average time/residue: 1.4128 time to fit residues: 456.7463 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 : 2.432 ------------------------------------------------------------------------------- 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 93 MET 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 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 109 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 194 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS E 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19248 Z= 0.207 Angle : 0.572 6.903 25956 Z= 0.309 Chirality : 0.044 0.180 2928 Planarity : 0.003 0.030 3072 Dihedral : 9.658 59.532 2796 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.05 % Allowed : 15.72 % Favored : 82.24 % 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: 2.79 (0.18), residues: 2196 helix: 2.69 (0.13), residues: 1596 sheet: 2.33 (0.41), residues: 132 loop : -1.51 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 133 HIS 0.005 0.001 HIS C 94 PHE 0.015 0.002 PHE H 51 TYR 0.018 0.002 TYR L 212 ARG 0.006 0.000 ARG K 216 *********************** 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 309 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6620 (t80) REVERT: B 136 TYR cc_start: 0.7392 (t80) cc_final: 0.7172 (t80) REVERT: B 212 TYR cc_start: 0.7420 (m-80) cc_final: 0.7142 (m-10) REVERT: C 22 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7782 (ttmm) REVERT: C 97 TYR cc_start: 0.7393 (t80) cc_final: 0.6905 (t80) REVERT: E 136 TYR cc_start: 0.7450 (t80) cc_final: 0.7034 (t80) REVERT: E 140 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8079 (mp) REVERT: I 97 TYR cc_start: 0.7724 (t80) cc_final: 0.7451 (t80) REVERT: J 22 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7751 (tppp) REVERT: J 97 TYR cc_start: 0.7522 (t80) cc_final: 0.6925 (t80) REVERT: K 22 LYS cc_start: 0.8305 (mtpp) cc_final: 0.7836 (ttmm) outliers start: 41 outliers final: 19 residues processed: 292 average time/residue: 1.3762 time to fit residues: 450.8583 Evaluate side-chains 279 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 2.121 ------------------------------------------------------------------------------- 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 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 140 ILE 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 J residue 212 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.0670 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 0.0020 chunk 131 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6928 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19248 Z= 0.165 Angle : 0.531 8.374 25956 Z= 0.286 Chirality : 0.043 0.171 2928 Planarity : 0.003 0.026 3072 Dihedral : 8.398 58.070 2786 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.50 % Allowed : 16.57 % Favored : 80.94 % 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: 3.17 (0.18), residues: 2196 helix: 3.03 (0.13), residues: 1596 sheet: 2.51 (0.43), residues: 132 loop : -1.64 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 133 HIS 0.004 0.000 HIS K 94 PHE 0.011 0.001 PHE K 51 TYR 0.019 0.001 TYR K 212 ARG 0.004 0.000 ARG K 216 *********************** 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 308 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 TYR cc_start: 0.7355 (m-80) cc_final: 0.6805 (t80) REVERT: C 22 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7725 (ttmm) REVERT: C 97 TYR cc_start: 0.7517 (t80) cc_final: 0.7008 (t80) REVERT: D 212 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6876 (t80) REVERT: F 159 ASP cc_start: 0.8235 (p0) cc_final: 0.7752 (p0) REVERT: F 212 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6767 (t80) REVERT: H 212 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6876 (t80) REVERT: J 22 LYS cc_start: 0.8245 (mtpp) cc_final: 0.7853 (ttmm) outliers start: 50 outliers final: 33 residues processed: 291 average time/residue: 1.3606 time to fit residues: 446.5332 Evaluate side-chains 285 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 208 THR 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 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 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 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 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 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 217 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 215 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 0.0970 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19248 Z= 0.289 Angle : 0.601 7.904 25956 Z= 0.327 Chirality : 0.046 0.180 2928 Planarity : 0.003 0.033 3072 Dihedral : 8.553 57.962 2784 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.89 % Allowed : 17.32 % Favored : 79.79 % 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: 3.10 (0.18), residues: 2196 helix: 2.96 (0.13), residues: 1596 sheet: 2.27 (0.42), residues: 132 loop : -1.50 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 133 HIS 0.007 0.001 HIS C 73 PHE 0.015 0.002 PHE K 51 TYR 0.019 0.002 TYR K 65 ARG 0.003 0.000 ARG L 165 *********************** 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 309 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6522 (t80) REVERT: B 212 TYR cc_start: 0.7458 (m-80) cc_final: 0.6873 (t80) REVERT: C 22 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7577 (ttmm) REVERT: C 97 TYR cc_start: 0.7574 (t80) cc_final: 0.7024 (t80) REVERT: D 212 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6908 (t80) REVERT: F 159 ASP cc_start: 0.8207 (p0) cc_final: 0.7835 (p0) REVERT: F 212 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6759 (t80) REVERT: G 8 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7175 (p) REVERT: G 159 ASP cc_start: 0.8195 (p0) cc_final: 0.7886 (p0) REVERT: H 212 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6893 (t80) REVERT: I 212 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6534 (m-10) REVERT: J 22 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7721 (ttmm) REVERT: L 212 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6781 (t80) REVERT: L 216 ARG cc_start: 0.7709 (tmm160) cc_final: 0.7394 (tmm160) outliers start: 58 outliers final: 37 residues processed: 289 average time/residue: 1.3422 time to fit residues: 435.4716 Evaluate side-chains 291 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER 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 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 140 ILE 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 G residue 215 ILE 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 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 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 70 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19248 Z= 0.208 Angle : 0.555 8.532 25956 Z= 0.303 Chirality : 0.044 0.167 2928 Planarity : 0.003 0.030 3072 Dihedral : 8.092 58.924 2784 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.84 % Allowed : 17.56 % Favored : 79.59 % 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: 3.28 (0.18), residues: 2196 helix: 3.12 (0.13), residues: 1596 sheet: 2.25 (0.42), residues: 132 loop : -1.52 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 133 HIS 0.005 0.001 HIS C 94 PHE 0.012 0.001 PHE K 51 TYR 0.013 0.002 TYR I 68 ARG 0.006 0.000 ARG J 216 *********************** 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 313 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6754 (t80) REVERT: B 212 TYR cc_start: 0.7458 (m-80) cc_final: 0.6916 (t80) REVERT: B 217 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5817 (t80) REVERT: C 22 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7717 (ttmm) REVERT: D 212 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6922 (t80) REVERT: F 159 ASP cc_start: 0.8222 (p0) cc_final: 0.7855 (p0) REVERT: F 212 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6807 (t80) REVERT: G 8 THR cc_start: 0.7372 (OUTLIER) cc_final: 0.7171 (p) REVERT: G 159 ASP cc_start: 0.8240 (p0) cc_final: 0.7825 (p0) REVERT: H 212 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6864 (t80) REVERT: J 22 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7786 (ttmm) REVERT: K 22 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7721 (mmmt) REVERT: L 212 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6642 (t80) outliers start: 57 outliers final: 39 residues processed: 293 average time/residue: 1.3608 time to fit residues: 447.9995 Evaluate side-chains 294 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER 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 B residue 217 TYR 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 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 93 MET Chi-restraints excluded: chain E residue 140 ILE 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 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 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 163 MET 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 201 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 130 optimal weight: 0.0030 chunk 126 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19248 Z= 0.184 Angle : 0.541 7.944 25956 Z= 0.294 Chirality : 0.043 0.173 2928 Planarity : 0.003 0.029 3072 Dihedral : 7.624 59.438 2784 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.89 % Allowed : 18.11 % Favored : 78.99 % 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: 3.38 (0.18), residues: 2196 helix: 3.21 (0.13), residues: 1596 sheet: 2.28 (0.42), residues: 132 loop : -1.57 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 133 HIS 0.004 0.001 HIS C 94 PHE 0.011 0.001 PHE K 51 TYR 0.013 0.001 TYR E 136 ARG 0.006 0.000 ARG J 216 *********************** 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 308 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6781 (t80) REVERT: B 212 TYR cc_start: 0.7601 (m-80) cc_final: 0.7052 (t80) REVERT: B 217 TYR cc_start: 0.6393 (OUTLIER) cc_final: 0.5841 (t80) REVERT: C 22 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7558 (ttmm) REVERT: C 209 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: D 212 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.7008 (t80) REVERT: F 159 ASP cc_start: 0.8210 (p0) cc_final: 0.7852 (p0) REVERT: F 212 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6767 (t80) REVERT: G 159 ASP cc_start: 0.8250 (p0) cc_final: 0.7872 (p0) REVERT: H 212 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6902 (t80) REVERT: J 22 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7735 (ttmm) REVERT: L 212 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6642 (t80) outliers start: 58 outliers final: 38 residues processed: 286 average time/residue: 1.3576 time to fit residues: 435.9232 Evaluate side-chains 291 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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 208 THR 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 209 GLU 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 211 CYS Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain E residue 215 ILE 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 G residue 85 SER Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 211 CYS 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 212 TYR Chi-restraints excluded: chain J residue 217 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 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 128 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19248 Z= 0.292 Angle : 0.605 9.070 25956 Z= 0.327 Chirality : 0.046 0.185 2928 Planarity : 0.003 0.033 3072 Dihedral : 7.728 59.837 2784 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.79 % Allowed : 18.41 % Favored : 78.79 % 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: 3.28 (0.18), residues: 2196 helix: 3.11 (0.13), residues: 1596 sheet: 2.14 (0.42), residues: 132 loop : -1.48 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 133 HIS 0.006 0.001 HIS C 73 PHE 0.015 0.002 PHE K 51 TYR 0.017 0.002 TYR A 65 ARG 0.008 0.001 ARG C 216 *********************** 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 301 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 245 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6846 (t80) REVERT: B 212 TYR cc_start: 0.7546 (m-80) cc_final: 0.7035 (t80) REVERT: C 22 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7491 (ttmm) REVERT: C 136 TYR cc_start: 0.7281 (t80) cc_final: 0.7040 (t80) REVERT: D 212 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6943 (t80) REVERT: F 159 ASP cc_start: 0.8248 (p0) cc_final: 0.7885 (p0) REVERT: F 212 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6808 (t80) REVERT: G 159 ASP cc_start: 0.8318 (p0) cc_final: 0.7944 (p0) REVERT: H 212 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6858 (t80) REVERT: I 212 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6575 (m-10) REVERT: K 22 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7756 (mmmt) REVERT: L 212 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6626 (t80) outliers start: 56 outliers final: 42 residues processed: 279 average time/residue: 1.3494 time to fit residues: 423.9571 Evaluate side-chains 290 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 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 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 211 CYS 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 E residue 215 ILE 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 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 211 CYS 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 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 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 Chi-restraints excluded: chain L residue 217 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 116 optimal weight: 0.2980 chunk 84 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3444 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: