Starting phenix.real_space_refine on Thu Mar 5 04:53:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qer_13938/03_2026/7qer_13938.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qer_13938/03_2026/7qer_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_13938/03_2026/7qer_13938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qer_13938/03_2026/7qer_13938.map" model { file = "/net/cci-nas-00/data/ceres_data/7qer_13938/03_2026/7qer_13938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qer_13938/03_2026/7qer_13938.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.84, per 1000 atoms: 0.25 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: 1.68 Conformation dependent library (CDL) restraints added in 802.4 milliseconds 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: 0.53 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: 2.97 Time building geometry restraints manager: 2.23 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'B' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'C' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'D' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'E' and (resid 4 through 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 301 or resid 303 through 304)) selection = (chain 'H' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'I' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'J' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'K' and (resid 4 through 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: 0.010 Normalize map: mean=0, sd=1: 3.710 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.950 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (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 ARG 0.002 0.000 ARG L 165 TYR 0.016 0.002 TYR F 65 PHE 0.020 0.002 PHE F 51 TRP 0.008 0.002 TRP K 172 HIS 0.003 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00867 (19248) covalent geometry : angle 0.93816 (25956) SS BOND : bond 0.00598 ( 36) SS BOND : angle 1.93578 ( 72) hydrogen bonds : bond 0.24705 ( 1308) hydrogen bonds : angle 7.22735 ( 3816) *********************** 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 : 0.739 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: 0.5769 time to fit residues: 206.5240 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 : 0.491 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.126999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.077012 restraints weight = 28377.999| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.89 r_work: 0.2840 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19284 Z= 0.176 Angle : 0.629 7.938 26028 Z= 0.336 Chirality : 0.043 0.152 2928 Planarity : 0.004 0.025 3072 Dihedral : 11.082 59.956 2813 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.25 % Allowed : 14.82 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.18), residues: 2196 helix: 2.11 (0.13), residues: 1572 sheet: 1.89 (0.39), residues: 132 loop : -1.39 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 216 TYR 0.014 0.002 TYR A 65 PHE 0.011 0.002 PHE K 51 TRP 0.005 0.001 TRP J 172 HIS 0.003 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00355 (19248) covalent geometry : angle 0.62689 (25956) SS BOND : bond 0.00248 ( 36) SS BOND : angle 1.16832 ( 72) hydrogen bonds : bond 0.08554 ( 1308) hydrogen bonds : angle 4.23500 ( 3816) *********************** 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 297 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8125 (mtm) cc_final: 0.7919 (mtt) REVERT: B 140 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7814 (mp) REVERT: B 216 ARG cc_start: 0.8008 (ttp-110) cc_final: 0.7555 (ttp80) REVERT: C 97 TYR cc_start: 0.7737 (t80) cc_final: 0.7266 (t80) REVERT: E 136 TYR cc_start: 0.7319 (t80) cc_final: 0.7093 (t80) REVERT: E 216 ARG cc_start: 0.7408 (tmm-80) cc_final: 0.7193 (tmm-80) REVERT: F 216 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7876 (tmm-80) REVERT: G 216 ARG cc_start: 0.7906 (tmm-80) cc_final: 0.7703 (tmm-80) REVERT: H 93 MET cc_start: 0.8018 (mtm) cc_final: 0.7763 (mtt) REVERT: I 97 TYR cc_start: 0.7743 (t80) cc_final: 0.7489 (t80) REVERT: I 140 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8190 (mp) REVERT: J 22 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7738 (tppp) REVERT: J 97 TYR cc_start: 0.7544 (t80) cc_final: 0.6995 (t80) REVERT: K 134 TRP cc_start: 0.8130 (m100) cc_final: 0.7828 (m-10) outliers start: 25 outliers final: 11 residues processed: 286 average time/residue: 0.6430 time to fit residues: 204.3885 Evaluate side-chains 264 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 G residue 212 TYR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I 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 55 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.127449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076835 restraints weight = 28683.312| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.90 r_work: 0.2837 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2559 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= 0.146 Angle : 0.567 7.422 26028 Z= 0.306 Chirality : 0.043 0.171 2928 Planarity : 0.003 0.030 3072 Dihedral : 10.030 59.973 2798 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.80 % Allowed : 15.77 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.18), residues: 2196 helix: 2.64 (0.13), residues: 1596 sheet: 2.29 (0.42), residues: 132 loop : -1.56 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 184 TYR 0.013 0.002 TYR H 65 PHE 0.013 0.002 PHE H 51 TRP 0.009 0.001 TRP D 133 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00310 (19248) covalent geometry : angle 0.56526 (25956) SS BOND : bond 0.00272 ( 36) SS BOND : angle 1.07665 ( 72) hydrogen bonds : bond 0.06868 ( 1308) hydrogen bonds : angle 3.90225 ( 3816) *********************** 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 306 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 TYR cc_start: 0.7360 (m-80) cc_final: 0.7067 (m-10) REVERT: C 97 TYR cc_start: 0.7506 (t80) cc_final: 0.7036 (t80) REVERT: E 136 TYR cc_start: 0.7460 (t80) cc_final: 0.7126 (t80) REVERT: E 209 GLU cc_start: 0.9016 (tt0) cc_final: 0.8713 (tt0) REVERT: H 139 SER cc_start: 0.8811 (t) cc_final: 0.8496 (p) REVERT: I 97 TYR cc_start: 0.7859 (t80) cc_final: 0.7615 (t80) REVERT: I 140 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8076 (mp) REVERT: J 22 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7755 (tppp) REVERT: J 97 TYR cc_start: 0.7570 (t80) cc_final: 0.7021 (t80) REVERT: K 22 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7875 (ttmm) REVERT: K 134 TRP cc_start: 0.8193 (m100) cc_final: 0.7878 (m-10) outliers start: 36 outliers final: 16 residues processed: 291 average time/residue: 0.6134 time to fit residues: 198.8737 Evaluate side-chains 276 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 211 CYS Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 215 ILE 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 L residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 174 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 149 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.129086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078953 restraints weight = 28349.341| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.88 r_work: 0.2886 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19284 Z= 0.125 Angle : 0.532 8.264 26028 Z= 0.285 Chirality : 0.042 0.164 2928 Planarity : 0.003 0.025 3072 Dihedral : 8.743 59.941 2788 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.40 % Allowed : 16.77 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.18), residues: 2196 helix: 3.00 (0.13), residues: 1596 sheet: 2.51 (0.43), residues: 132 loop : -1.66 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 184 TYR 0.009 0.001 TYR G 158 PHE 0.010 0.001 PHE A 31 TRP 0.009 0.001 TRP D 133 HIS 0.004 0.000 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00250 (19248) covalent geometry : angle 0.53024 (25956) SS BOND : bond 0.00205 ( 36) SS BOND : angle 0.87502 ( 72) hydrogen bonds : bond 0.05636 ( 1308) hydrogen bonds : angle 3.65876 ( 3816) *********************** 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 313 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 TYR cc_start: 0.7295 (m-80) cc_final: 0.6834 (t80) REVERT: C 97 TYR cc_start: 0.7584 (t80) cc_final: 0.7105 (t80) REVERT: D 212 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6668 (t80) REVERT: E 140 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7713 (mp) REVERT: F 159 ASP cc_start: 0.8638 (p0) cc_final: 0.8217 (p0) REVERT: F 212 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6720 (t80) REVERT: H 42 GLU cc_start: 0.8421 (pt0) cc_final: 0.8155 (pm20) REVERT: I 97 TYR cc_start: 0.7968 (t80) cc_final: 0.7747 (t80) REVERT: J 22 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7780 (ttmm) REVERT: J 97 TYR cc_start: 0.7606 (t80) cc_final: 0.7020 (t80) REVERT: K 134 TRP cc_start: 0.8191 (m100) cc_final: 0.7874 (m-10) REVERT: L 212 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.6368 (t80) outliers start: 48 outliers final: 30 residues processed: 293 average time/residue: 0.6083 time to fit residues: 199.9039 Evaluate side-chains 282 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 93 MET 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 H residue 38 VAL Chi-restraints excluded: chain H residue 208 THR 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 93 MET Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 211 CYS 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 87 optimal weight: 2.9990 chunk 166 optimal weight: 0.0170 chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 138 optimal weight: 0.1980 chunk 168 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 159 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.129161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079350 restraints weight = 28556.045| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.90 r_work: 0.2894 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19284 Z= 0.118 Angle : 0.521 8.797 26028 Z= 0.279 Chirality : 0.042 0.168 2928 Planarity : 0.003 0.022 3072 Dihedral : 7.753 59.500 2786 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.94 % Allowed : 16.77 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.18), residues: 2196 helix: 3.20 (0.13), residues: 1596 sheet: 2.59 (0.43), residues: 132 loop : -1.67 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 216 TYR 0.010 0.001 TYR H 65 PHE 0.011 0.001 PHE H 31 TRP 0.009 0.001 TRP D 133 HIS 0.004 0.000 HIS K 94 Details of bonding type rmsd covalent geometry : bond 0.00238 (19248) covalent geometry : angle 0.52028 (25956) SS BOND : bond 0.00196 ( 36) SS BOND : angle 0.82413 ( 72) hydrogen bonds : bond 0.05253 ( 1308) hydrogen bonds : angle 3.60096 ( 3816) *********************** 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 318 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 259 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8292 (pt0) cc_final: 0.8090 (pm20) REVERT: A 212 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6627 (t80) REVERT: B 212 TYR cc_start: 0.7363 (m-80) cc_final: 0.6910 (t80) REVERT: C 97 TYR cc_start: 0.7633 (t80) cc_final: 0.7107 (t80) REVERT: D 212 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6665 (t80) REVERT: F 212 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6641 (t80) REVERT: H 42 GLU cc_start: 0.8362 (pt0) cc_final: 0.8120 (pm20) REVERT: H 212 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6776 (t80) REVERT: L 212 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6364 (t80) outliers start: 59 outliers final: 35 residues processed: 294 average time/residue: 0.5877 time to fit residues: 193.5157 Evaluate side-chains 290 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 93 MET 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 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 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 208 THR 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 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 211 CYS 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 190 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.127731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076941 restraints weight = 28113.177| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.87 r_work: 0.2842 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3169 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= 0.146 Angle : 0.555 9.490 26028 Z= 0.300 Chirality : 0.043 0.172 2928 Planarity : 0.003 0.026 3072 Dihedral : 7.494 59.448 2784 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.74 % Allowed : 18.11 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.18), residues: 2196 helix: 3.17 (0.13), residues: 1596 sheet: 2.45 (0.43), residues: 132 loop : -1.57 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 216 TYR 0.023 0.002 TYR K 217 PHE 0.011 0.002 PHE K 51 TRP 0.009 0.001 TRP D 133 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00326 (19248) covalent geometry : angle 0.55329 (25956) SS BOND : bond 0.00320 ( 36) SS BOND : angle 1.04831 ( 72) hydrogen bonds : bond 0.05901 ( 1308) hydrogen bonds : angle 3.68570 ( 3816) *********************** 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 298 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6646 (t80) REVERT: B 212 TYR cc_start: 0.7426 (m-80) cc_final: 0.6980 (t80) REVERT: B 217 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5810 (t80) REVERT: D 212 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6660 (t80) REVERT: F 159 ASP cc_start: 0.8689 (p0) cc_final: 0.8371 (p0) REVERT: F 212 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6702 (t80) REVERT: G 8 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7402 (p) REVERT: G 159 ASP cc_start: 0.8634 (p0) cc_final: 0.8284 (p0) REVERT: H 42 GLU cc_start: 0.8372 (pt0) cc_final: 0.8161 (pm20) REVERT: H 212 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6761 (t80) REVERT: J 22 LYS cc_start: 0.8106 (ttmm) cc_final: 0.7893 (tppp) REVERT: L 212 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6418 (t80) outliers start: 55 outliers final: 35 residues processed: 278 average time/residue: 0.6104 time to fit residues: 190.3094 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 : 0.703 ------------------------------------------------------------------------------- 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 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 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 F residue 85 SER 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 211 CYS 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 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 211 CYS 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 76 optimal weight: 0.0070 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 13 optimal weight: 0.0050 overall best weight: 0.5612 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.129389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078993 restraints weight = 28080.768| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.86 r_work: 0.2885 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19284 Z= 0.117 Angle : 0.514 7.248 26028 Z= 0.277 Chirality : 0.041 0.163 2928 Planarity : 0.003 0.022 3072 Dihedral : 6.750 56.907 2784 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.94 % Allowed : 18.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.18), residues: 2196 helix: 3.33 (0.13), residues: 1596 sheet: 2.50 (0.43), residues: 132 loop : -1.60 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 98 TYR 0.009 0.001 TYR E 68 PHE 0.009 0.001 PHE E 31 TRP 0.008 0.001 TRP D 133 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00239 (19248) covalent geometry : angle 0.51287 (25956) SS BOND : bond 0.00197 ( 36) SS BOND : angle 0.83489 ( 72) hydrogen bonds : bond 0.05089 ( 1308) hydrogen bonds : angle 3.54632 ( 3816) *********************** 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: 59 poor density : 249 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.6594 (t80) REVERT: B 212 TYR cc_start: 0.7444 (m-80) cc_final: 0.7055 (t80) REVERT: C 99 ARG cc_start: 0.7696 (mmt180) cc_final: 0.7304 (ttp80) REVERT: D 209 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: D 212 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6737 (t80) REVERT: E 93 MET cc_start: 0.7916 (mmm) cc_final: 0.7639 (ttm) REVERT: E 98 ARG cc_start: 0.6560 (tpp-160) cc_final: 0.6314 (tpp80) REVERT: E 140 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7788 (mp) REVERT: F 159 ASP cc_start: 0.8691 (p0) cc_final: 0.8356 (p0) REVERT: F 209 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8815 (tp30) REVERT: F 212 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6561 (t80) REVERT: F 215 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8187 (tp) REVERT: G 8 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7402 (p) REVERT: G 159 ASP cc_start: 0.8681 (p0) cc_final: 0.8290 (p0) REVERT: G 212 TYR cc_start: 0.6690 (OUTLIER) cc_final: 0.6289 (t80) REVERT: H 212 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6721 (t80) REVERT: J 22 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7829 (tppp) REVERT: L 212 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6337 (t80) outliers start: 59 outliers final: 37 residues processed: 279 average time/residue: 0.6313 time to fit residues: 196.8097 Evaluate side-chains 288 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 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 208 THR Chi-restraints excluded: chain D residue 209 GLU 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 211 CYS Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 209 GLU 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 211 CYS Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 93 MET 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 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 211 CYS 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 203 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.127692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076693 restraints weight = 28199.247| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.87 r_work: 0.2830 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3306 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= 0.151 Angle : 0.562 9.438 26028 Z= 0.302 Chirality : 0.043 0.177 2928 Planarity : 0.003 0.027 3072 Dihedral : 6.755 58.525 2784 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.79 % Allowed : 18.66 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.48 (0.18), residues: 2196 helix: 3.27 (0.13), residues: 1596 sheet: 2.39 (0.43), residues: 132 loop : -1.52 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 216 TYR 0.016 0.002 TYR D 65 PHE 0.012 0.002 PHE B 191 TRP 0.009 0.001 TRP D 133 HIS 0.005 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00342 (19248) covalent geometry : angle 0.55934 (25956) SS BOND : bond 0.00338 ( 36) SS BOND : angle 1.10444 ( 72) hydrogen bonds : bond 0.05922 ( 1308) hydrogen bonds : angle 3.70375 ( 3816) *********************** 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 303 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.6613 (t80) REVERT: B 212 TYR cc_start: 0.7484 (m-80) cc_final: 0.7094 (t80) REVERT: B 217 TYR cc_start: 0.6046 (OUTLIER) cc_final: 0.5514 (t80) REVERT: D 212 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6706 (t80) REVERT: E 93 MET cc_start: 0.7836 (mmm) cc_final: 0.7512 (ttm) REVERT: E 98 ARG cc_start: 0.6593 (tpp-160) cc_final: 0.6286 (tpp80) REVERT: E 140 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7786 (mp) REVERT: F 159 ASP cc_start: 0.8703 (p0) cc_final: 0.8351 (p0) REVERT: F 212 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6563 (t80) REVERT: F 215 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8233 (tp) REVERT: G 8 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7420 (p) REVERT: G 159 ASP cc_start: 0.8704 (p0) cc_final: 0.8331 (p0) REVERT: G 212 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.6354 (t80) REVERT: H 212 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6822 (t80) REVERT: J 22 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7781 (tppp) REVERT: L 212 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6332 (t80) outliers start: 56 outliers final: 36 residues processed: 281 average time/residue: 0.6071 time to fit residues: 191.4293 Evaluate side-chains 289 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 A residue 215 ILE 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 D residue 85 SER 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 140 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 85 SER 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 93 MET 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 215 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 0.6980 chunk 202 optimal weight: 0.0040 chunk 66 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.129081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078577 restraints weight = 28152.374| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.87 r_work: 0.2874 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19284 Z= 0.119 Angle : 0.523 7.782 26028 Z= 0.281 Chirality : 0.042 0.175 2928 Planarity : 0.003 0.026 3072 Dihedral : 6.173 57.349 2784 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.50 % Allowed : 18.86 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.64 (0.18), residues: 2196 helix: 3.42 (0.13), residues: 1596 sheet: 2.44 (0.43), residues: 132 loop : -1.56 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 216 TYR 0.010 0.001 TYR E 68 PHE 0.009 0.001 PHE I 31 TRP 0.008 0.001 TRP D 133 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00248 (19248) covalent geometry : angle 0.52193 (25956) SS BOND : bond 0.00219 ( 36) SS BOND : angle 0.86315 ( 72) hydrogen bonds : bond 0.05136 ( 1308) hydrogen bonds : angle 3.55826 ( 3816) *********************** 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 297 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.6599 (t80) REVERT: B 212 TYR cc_start: 0.7496 (m-80) cc_final: 0.7126 (t80) REVERT: C 42 GLU cc_start: 0.8218 (tp30) cc_final: 0.7936 (tp30) REVERT: C 99 ARG cc_start: 0.7713 (mmt180) cc_final: 0.7310 (ttp80) REVERT: D 212 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6768 (t80) REVERT: E 93 MET cc_start: 0.7907 (mmm) cc_final: 0.7654 (ttm) REVERT: E 98 ARG cc_start: 0.6606 (tpp-160) cc_final: 0.6284 (tpp80) REVERT: E 216 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6555 (tmm-80) REVERT: F 154 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8069 (t80) REVERT: F 159 ASP cc_start: 0.8702 (p0) cc_final: 0.8333 (p0) REVERT: F 212 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6530 (t80) REVERT: G 8 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7422 (p) REVERT: G 159 ASP cc_start: 0.8681 (p0) cc_final: 0.8275 (p0) REVERT: G 212 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.6359 (t80) REVERT: H 212 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6747 (t80) REVERT: L 212 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6413 (t80) outliers start: 50 outliers final: 33 residues processed: 273 average time/residue: 0.6421 time to fit residues: 195.7564 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 : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR 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 A residue 215 ILE Chi-restraints excluded: chain B residue 85 SER 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 C residue 217 TYR 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 208 THR Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain F residue 154 PHE 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 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 93 MET 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 93 MET Chi-restraints excluded: chain J residue 212 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 203 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.128542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077966 restraints weight = 28135.485| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.86 r_work: 0.2859 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3495 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= 0.127 Angle : 0.540 9.656 26028 Z= 0.288 Chirality : 0.043 0.181 2928 Planarity : 0.003 0.027 3072 Dihedral : 5.941 51.918 2784 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.15 % Allowed : 19.16 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.77 (0.18), residues: 2196 helix: 3.31 (0.12), residues: 1656 sheet: 2.44 (0.43), residues: 132 loop : -1.33 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 216 TYR 0.012 0.001 TYR D 65 PHE 0.011 0.001 PHE K 51 TRP 0.008 0.001 TRP D 133 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00276 (19248) covalent geometry : angle 0.53866 (25956) SS BOND : bond 0.00259 ( 36) SS BOND : angle 0.91895 ( 72) hydrogen bonds : bond 0.05339 ( 1308) hydrogen bonds : angle 3.61115 ( 3816) ********************** 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 288 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6615 (t80) REVERT: B 212 TYR cc_start: 0.7391 (m-80) cc_final: 0.7048 (t80) REVERT: C 42 GLU cc_start: 0.8386 (tp30) cc_final: 0.8018 (tp30) REVERT: C 99 ARG cc_start: 0.7760 (mmt180) cc_final: 0.7336 (ttp80) REVERT: D 212 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6751 (t80) REVERT: E 93 MET cc_start: 0.7851 (mmm) cc_final: 0.7566 (ttm) REVERT: E 98 ARG cc_start: 0.6582 (tpp-160) cc_final: 0.6263 (tpp80) REVERT: E 140 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7841 (mp) REVERT: F 159 ASP cc_start: 0.8716 (p0) cc_final: 0.8266 (p0) REVERT: F 212 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6536 (t80) REVERT: G 8 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7427 (p) REVERT: G 159 ASP cc_start: 0.8712 (p0) cc_final: 0.8230 (p0) REVERT: G 212 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6341 (t80) REVERT: H 212 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6732 (t80) REVERT: I 212 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: L 212 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.6445 (t80) outliers start: 43 outliers final: 29 residues processed: 269 average time/residue: 0.6279 time to fit residues: 188.3756 Evaluate side-chains 275 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR 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 93 MET Chi-restraints excluded: chain C residue 212 TYR 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 140 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain E residue 216 ARG 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 208 THR Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 93 MET 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 93 MET Chi-restraints excluded: chain J residue 212 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 155 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 76 optimal weight: 0.0270 chunk 114 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.129503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078950 restraints weight = 28238.478| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.86 r_work: 0.2884 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19284 Z= 0.117 Angle : 0.522 8.266 26028 Z= 0.280 Chirality : 0.042 0.178 2928 Planarity : 0.003 0.042 3072 Dihedral : 5.440 52.147 2784 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.10 % Allowed : 19.26 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.87 (0.18), residues: 2196 helix: 3.39 (0.12), residues: 1656 sheet: 2.50 (0.43), residues: 132 loop : -1.35 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 216 TYR 0.009 0.001 TYR E 68 PHE 0.010 0.001 PHE I 31 TRP 0.008 0.001 TRP D 133 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00244 (19248) covalent geometry : angle 0.52094 (25956) SS BOND : bond 0.00208 ( 36) SS BOND : angle 0.82920 ( 72) hydrogen bonds : bond 0.04929 ( 1308) hydrogen bonds : angle 3.53653 ( 3816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9841.54 seconds wall clock time: 167 minutes 43.23 seconds (10063.23 seconds total)