Starting phenix.real_space_refine on Sun Jun 29 09:56:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpv_16787/06_2025/8cpv_16787.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpv_16787/06_2025/8cpv_16787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cpv_16787/06_2025/8cpv_16787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpv_16787/06_2025/8cpv_16787.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpv_16787/06_2025/8cpv_16787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpv_16787/06_2025/8cpv_16787.cif" } resolution = 1.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Mg 14 5.21 5 S 168 5.16 5 Na 24 4.78 5 C 21312 2.51 5 N 5976 2.21 5 O 8361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 35855 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "2" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "4" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "6" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "F" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "M" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "O" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "Q" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "S" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "X" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "a" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "e" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "r" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 21.84, per 1000 atoms: 0.61 Number of scatterers: 35855 At special positions: 0 Unit cell: (131.856, 131.856, 131.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 Mg 14 11.99 Na 24 11.00 O 8361 8.00 N 5976 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 10.01 Conformation dependent library (CDL) restraints added in 4.5 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 Processing helix chain '1' and resid 48 through 77 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 163 through 174 Processing helix chain '2' and resid 13 through 42 Processing helix chain '2' and resid 48 through 77 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 163 through 174 Processing helix chain '4' and resid 13 through 42 Processing helix chain '4' and resid 48 through 77 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 163 through 174 Processing helix chain '6' and resid 13 through 42 Processing helix chain '6' and resid 48 through 77 Processing helix chain '6' and resid 95 through 124 Processing helix chain '6' and resid 126 through 137 Processing helix chain '6' and resid 137 through 159 Processing helix chain '6' and resid 163 through 174 Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 77 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 77 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 77 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 77 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 77 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 77 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 77 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 77 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 77 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 77 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 77 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 Processing helix chain 'a' and resid 13 through 42 Processing helix chain 'a' and resid 48 through 77 Processing helix chain 'a' and resid 95 through 124 Processing helix chain 'a' and resid 126 through 137 Processing helix chain 'a' and resid 137 through 159 Processing helix chain 'a' and resid 163 through 174 Processing helix chain 'e' and resid 13 through 42 Processing helix chain 'e' and resid 48 through 77 Processing helix chain 'e' and resid 95 through 124 Processing helix chain 'e' and resid 126 through 137 Processing helix chain 'e' and resid 137 through 159 Processing helix chain 'e' and resid 163 through 174 Processing helix chain 'r' and resid 13 through 42 Processing helix chain 'r' and resid 48 through 77 Processing helix chain 'r' and resid 95 through 124 Processing helix chain 'r' and resid 126 through 137 Processing helix chain 'r' and resid 137 through 159 Processing helix chain 'r' and resid 163 through 174 2710 hydrogen bonds defined for protein. 8130 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: 11.63 Time building geometry restraints manager: 11.28 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: 11634 1.34 - 1.46: 6193 1.46 - 1.58: 16685 1.58 - 1.70: 0 1.70 - 1.82: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX r 90 " pdb=" SG CSX r 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB CSX 1 90 " pdb=" SG CSX 1 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB CSX P 90 " pdb=" SG CSX P 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB CSX A 90 " pdb=" SG CSX A 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB CSX 6 90 " pdb=" SG CSX 6 90 " ideal model delta sigma weight residual 1.831 1.760 0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 43387 1.55 - 3.10: 2779 3.10 - 4.65: 485 4.65 - 6.20: 152 6.20 - 7.76: 45 Bond angle restraints: 46848 Sorted by residual: angle pdb=" C ARG 6 63 " pdb=" CA ARG 6 63 " pdb=" CB ARG 6 63 " ideal model delta sigma weight residual 110.79 104.09 6.70 1.66e+00 3.63e-01 1.63e+01 angle pdb=" C TYR O 32 " pdb=" CA TYR O 32 " pdb=" CB TYR O 32 " ideal model delta sigma weight residual 110.85 117.41 -6.56 1.70e+00 3.46e-01 1.49e+01 angle pdb=" C TYR E 32 " pdb=" CA TYR E 32 " pdb=" CB TYR E 32 " ideal model delta sigma weight residual 110.85 117.37 -6.52 1.70e+00 3.46e-01 1.47e+01 angle pdb=" C TYR 4 32 " pdb=" CA TYR 4 32 " pdb=" CB TYR 4 32 " ideal model delta sigma weight residual 110.85 117.37 -6.52 1.70e+00 3.46e-01 1.47e+01 angle pdb=" C TYR I 32 " pdb=" CA TYR I 32 " pdb=" CB TYR I 32 " ideal model delta sigma weight residual 110.85 117.37 -6.52 1.70e+00 3.46e-01 1.47e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 19390 17.95 - 35.90: 1284 35.90 - 53.86: 165 53.86 - 71.81: 25 71.81 - 89.76: 136 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL a 46 " pdb=" C VAL a 46 " pdb=" N ALA a 47 " pdb=" CA ALA a 47 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL E 46 " pdb=" C VAL E 46 " pdb=" N ALA E 47 " pdb=" CA ALA E 47 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL K 46 " pdb=" C VAL K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3891 0.070 - 0.141: 821 0.141 - 0.211: 167 0.211 - 0.281: 24 0.281 - 0.352: 17 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CG LEU H 72 " pdb=" CB LEU H 72 " pdb=" CD1 LEU H 72 " pdb=" CD2 LEU H 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CG LEU I 72 " pdb=" CB LEU I 72 " pdb=" CD1 LEU I 72 " pdb=" CD2 LEU I 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CG LEU 1 72 " pdb=" CB LEU 1 72 " pdb=" CD1 LEU 1 72 " pdb=" CD2 LEU 1 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 32 " 0.056 2.00e-02 2.50e+03 5.46e-02 5.96e+01 pdb=" CG TYR I 32 " -0.134 2.00e-02 2.50e+03 pdb=" CD1 TYR I 32 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR I 32 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR I 32 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR I 32 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR I 32 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR I 32 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 32 " 0.056 2.00e-02 2.50e+03 5.46e-02 5.96e+01 pdb=" CG TYR U 32 " -0.133 2.00e-02 2.50e+03 pdb=" CD1 TYR U 32 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR U 32 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR U 32 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR U 32 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR U 32 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR U 32 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " -0.056 2.00e-02 2.50e+03 5.46e-02 5.95e+01 pdb=" CG TYR F 32 " 0.134 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 3067 2.73 - 3.27: 39689 3.27 - 3.81: 71135 3.81 - 4.36: 89873 4.36 - 4.90: 140342 Nonbonded interactions: 344106 Sorted by model distance: nonbonded pdb=" O HOH F 655 " pdb=" O HOH F 659 " model vdw 2.182 3.040 nonbonded pdb=" O HOH Y 656 " pdb=" O HOH Y 661 " model vdw 2.183 3.040 nonbonded pdb=" O HOH W 654 " pdb=" O HOH W 659 " model vdw 2.183 3.040 nonbonded pdb=" O HOH H 757 " pdb=" O HOH H 761 " model vdw 2.185 3.040 nonbonded pdb=" O CSX G 90 " pdb=" O HOH G 301 " model vdw 2.206 3.040 ... (remaining 344101 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: 0.01 Found NCS groups: ncs_group { reference = (chain '1' and (resid 4 through 176 or resid 201)) selection = (chain '2' and (resid 4 through 176 or resid 201)) selection = (chain '4' and (resid 4 through 176 or resid 201)) selection = (chain '6' and (resid 4 through 176 or resid 201)) selection = (chain 'A' and (resid 4 through 176 or resid 500)) selection = (chain 'B' and (resid 4 through 176 or resid 500)) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and (resid 4 through 176 or resid 201)) selection = (chain 'H' and (resid 4 through 176 or resid 201)) selection = chain 'I' selection = chain 'K' selection = (chain 'M' and (resid 4 through 176 or resid 201)) selection = (chain 'O' and (resid 4 through 176 or resid 500)) selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.720 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 77.220 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 34776 Z= 0.303 Angle : 0.908 7.756 46848 Z= 0.512 Chirality : 0.066 0.352 4920 Planarity : 0.009 0.066 6192 Dihedral : 14.406 89.761 13032 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.13), residues: 4032 helix: 1.60 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.94 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP I 93 HIS 0.015 0.003 HIS X 128 PHE 0.042 0.005 PHE M 41 TYR 0.134 0.010 TYR G 32 ARG 0.020 0.003 ARG W 63 Details of bonding type rmsd hydrogen bonds : bond 0.07802 ( 2710) hydrogen bonds : angle 4.66112 ( 8130) covalent geometry : bond 0.00630 (34776) covalent geometry : angle 0.90778 (46848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 5.223 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 2.6446 time to fit residues: 1875.5410 Evaluate side-chains 438 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 4.9990 chunk 309 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.144183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.141007 restraints weight = 18107.620| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 0.18 r_work: 0.3215 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.2970 rms_B_bonded: 2.49 restraints_weight: 0.1250 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34776 Z= 0.171 Angle : 0.650 6.235 46848 Z= 0.356 Chirality : 0.041 0.155 4920 Planarity : 0.005 0.049 6192 Dihedral : 4.671 19.990 4536 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.95 (0.13), residues: 4032 helix: 2.99 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.86 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP P 93 HIS 0.005 0.001 HIS X 128 PHE 0.025 0.003 PHE E 41 TYR 0.053 0.004 TYR A 32 ARG 0.011 0.001 ARG 2 63 Details of bonding type rmsd hydrogen bonds : bond 0.06160 ( 2710) hydrogen bonds : angle 4.02463 ( 8130) covalent geometry : bond 0.00336 (34776) covalent geometry : angle 0.64968 (46848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 4.242 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 2.3491 time to fit residues: 1232.6324 Evaluate side-chains 433 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 7.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 89 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 311 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 355 optimal weight: 1.9990 chunk 391 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 386 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 112 GLN 4 112 GLN 6 112 GLN A 112 GLN B 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN I 112 GLN K 112 GLN M 112 GLN O 112 GLN P 112 GLN Q 112 GLN S 112 GLN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN a 112 GLN e 112 GLN r 112 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.145454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.142853 restraints weight = 18530.598| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 0.16 r_work: 0.3258 rms_B_bonded: 0.70 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.3025 rms_B_bonded: 2.36 restraints_weight: 0.1250 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34776 Z= 0.137 Angle : 0.571 5.841 46848 Z= 0.314 Chirality : 0.037 0.141 4920 Planarity : 0.003 0.022 6192 Dihedral : 4.428 20.291 4536 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.58 (0.13), residues: 4032 helix: 3.48 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.75 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 93 HIS 0.004 0.001 HIS U 128 PHE 0.020 0.003 PHE 6 41 TYR 0.028 0.003 TYR A 32 ARG 0.005 0.001 ARG 2 63 Details of bonding type rmsd hydrogen bonds : bond 0.05572 ( 2710) hydrogen bonds : angle 3.81014 ( 8130) covalent geometry : bond 0.00260 (34776) covalent geometry : angle 0.57149 (46848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 4.358 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 2.1685 time to fit residues: 1216.2849 Evaluate side-chains 452 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 88 optimal weight: 6.9990 chunk 317 optimal weight: 5.9990 chunk 313 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 331 optimal weight: 8.9990 chunk 401 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 392 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 60 HIS 2 112 GLN 4 112 GLN 6 60 HIS 6 112 GLN A 112 GLN B 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN I 112 GLN K 112 GLN M 112 GLN O 112 GLN P 112 GLN Q 60 HIS Q 112 GLN S 112 GLN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN a 112 GLN e 112 GLN r 112 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.142193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.139522 restraints weight = 18350.000| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 0.17 r_work: 0.3191 rms_B_bonded: 0.85 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.2967 rms_B_bonded: 2.53 restraints_weight: 0.1250 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 34776 Z= 0.244 Angle : 0.749 6.835 46848 Z= 0.409 Chirality : 0.042 0.145 4920 Planarity : 0.005 0.050 6192 Dihedral : 4.514 18.844 4536 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.12), residues: 4032 helix: 2.95 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.56 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 93 HIS 0.010 0.002 HIS Q 60 PHE 0.029 0.004 PHE E 41 TYR 0.028 0.005 TYR B 137 ARG 0.011 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.07010 ( 2710) hydrogen bonds : angle 4.24981 ( 8130) covalent geometry : bond 0.00503 (34776) covalent geometry : angle 0.74931 (46848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 4.148 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 2.0750 time to fit residues: 1089.4715 Evaluate side-chains 457 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 60 HIS 2 112 GLN 4 112 GLN 6 60 HIS 6 112 GLN A 112 GLN B 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN I 112 GLN K 112 GLN M 112 GLN O 112 GLN P 112 GLN Q 60 HIS Q 112 GLN S 112 GLN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN a 112 GLN e 112 GLN r 112 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.146468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.143790 restraints weight = 18523.248| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 0.17 r_work: 0.3278 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work: 0.3043 rms_B_bonded: 2.32 restraints_weight: 0.1250 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 34776 Z= 0.126 Angle : 0.547 5.762 46848 Z= 0.298 Chirality : 0.036 0.137 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.365 20.513 4536 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.75 (0.13), residues: 4032 helix: 3.62 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.69 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 93 HIS 0.003 0.001 HIS 1 128 PHE 0.016 0.002 PHE 4 41 TYR 0.017 0.002 TYR A 137 ARG 0.003 0.000 ARG U 156 Details of bonding type rmsd hydrogen bonds : bond 0.05320 ( 2710) hydrogen bonds : angle 3.74751 ( 8130) covalent geometry : bond 0.00233 (34776) covalent geometry : angle 0.54672 (46848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 4.331 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 2.3444 time to fit residues: 1316.0535 Evaluate side-chains 433 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 181 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 407 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 349 optimal weight: 7.9990 chunk 402 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 112 GLN 4 112 GLN 6 112 GLN A 112 GLN B 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN I 112 GLN K 112 GLN M 112 GLN O 112 GLN P 112 GLN Q 112 GLN S 112 GLN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN a 112 GLN e 112 GLN r 112 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.144773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.142179 restraints weight = 18335.691| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 0.15 r_work: 0.3258 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work: 0.3017 rms_B_bonded: 2.32 restraints_weight: 0.1250 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34776 Z= 0.158 Angle : 0.605 6.176 46848 Z= 0.332 Chirality : 0.038 0.139 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.382 19.828 4536 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.54 (0.13), residues: 4032 helix: 3.46 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.70 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP S 93 HIS 0.003 0.001 HIS E 128 PHE 0.021 0.003 PHE E 41 TYR 0.019 0.003 TYR 2 137 ARG 0.005 0.001 ARG K 156 Details of bonding type rmsd hydrogen bonds : bond 0.05965 ( 2710) hydrogen bonds : angle 3.90745 ( 8130) covalent geometry : bond 0.00310 (34776) covalent geometry : angle 0.60496 (46848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 4.514 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 476 average time/residue: 2.1649 time to fit residues: 1180.2065 Evaluate side-chains 461 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 368 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 112 GLN 4 112 GLN 6 112 GLN A 112 GLN B 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN I 112 GLN K 112 GLN M 112 GLN O 112 GLN P 112 GLN Q 112 GLN S 112 GLN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN a 112 GLN e 112 GLN r 112 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.145705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.143097 restraints weight = 18412.530| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 0.16 r_work: 0.3264 rms_B_bonded: 0.68 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.3030 rms_B_bonded: 2.35 restraints_weight: 0.1250 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34776 Z= 0.142 Angle : 0.573 6.355 46848 Z= 0.315 Chirality : 0.037 0.136 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.349 20.027 4536 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.66 (0.13), residues: 4032 helix: 3.54 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.72 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 93 HIS 0.003 0.001 HIS P 128 PHE 0.019 0.003 PHE 4 41 TYR 0.018 0.002 TYR r 137 ARG 0.005 0.001 ARG H 156 Details of bonding type rmsd hydrogen bonds : bond 0.05634 ( 2710) hydrogen bonds : angle 3.82197 ( 8130) covalent geometry : bond 0.00273 (34776) covalent geometry : angle 0.57330 (46848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 4.194 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 2.1624 time to fit residues: 1188.5077 Evaluate side-chains 475 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 96 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 330 optimal weight: 0.9990 chunk 288 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 407 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 112 GLN 4 112 GLN 6 112 GLN A 112 GLN B 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN I 112 GLN K 112 GLN M 112 GLN O 112 GLN P 112 GLN Q 112 GLN S 112 GLN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN a 112 GLN e 112 GLN r 112 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.144494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.141859 restraints weight = 18259.171| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 0.16 r_work: 0.3252 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work: 0.3012 rms_B_bonded: 2.32 restraints_weight: 0.1250 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34776 Z= 0.169 Angle : 0.640 6.616 46848 Z= 0.346 Chirality : 0.039 0.139 4920 Planarity : 0.004 0.026 6192 Dihedral : 4.382 19.646 4536 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.13), residues: 4032 helix: 3.36 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.64 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP e 93 HIS 0.004 0.001 HIS K 128 PHE 0.023 0.003 PHE 4 41 TYR 0.021 0.003 TYR P 39 ARG 0.006 0.001 ARG X 156 Details of bonding type rmsd hydrogen bonds : bond 0.06141 ( 2710) hydrogen bonds : angle 3.95461 ( 8130) covalent geometry : bond 0.00339 (34776) covalent geometry : angle 0.64006 (46848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 4.063 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 2.0396 time to fit residues: 1067.6827 Evaluate side-chains 456 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 4.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 275 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 295 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 388 optimal weight: 0.8980 chunk 351 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 112 GLN 4 112 GLN 6 112 GLN A 112 GLN B 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN I 112 GLN K 112 GLN M 112 GLN O 112 GLN P 112 GLN Q 112 GLN S 112 GLN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN a 112 GLN e 112 GLN r 112 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.146066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.143540 restraints weight = 18368.393| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 0.15 r_work: 0.3274 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 1.33 restraints_weight: 0.2500 r_work: 0.3038 rms_B_bonded: 2.33 restraints_weight: 0.1250 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34776 Z= 0.137 Angle : 0.579 6.012 46848 Z= 0.313 Chirality : 0.037 0.136 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.339 20.069 4536 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.68 (0.13), residues: 4032 helix: 3.57 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.63 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP X 93 HIS 0.003 0.001 HIS 2 128 PHE 0.019 0.003 PHE e 41 TYR 0.017 0.002 TYR r 137 ARG 0.005 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.05490 ( 2710) hydrogen bonds : angle 3.78730 ( 8130) covalent geometry : bond 0.00266 (34776) covalent geometry : angle 0.57897 (46848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 4.786 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 2.0758 time to fit residues: 1106.4792 Evaluate side-chains 436 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 4.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 296 optimal weight: 0.0170 chunk 324 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 407 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 112 GLN 4 112 GLN 6 112 GLN A 112 GLN B 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN I 112 GLN K 112 GLN M 112 GLN O 112 GLN P 112 GLN Q 112 GLN S 112 GLN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN a 112 GLN e 112 GLN r 112 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.144047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.141402 restraints weight = 18302.654| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 0.16 r_work: 0.3248 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 1.36 restraints_weight: 0.2500 r_work: 0.3005 rms_B_bonded: 2.35 restraints_weight: 0.1250 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34776 Z= 0.180 Angle : 0.656 6.342 46848 Z= 0.357 Chirality : 0.039 0.139 4920 Planarity : 0.004 0.032 6192 Dihedral : 4.378 19.538 4536 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.13), residues: 4032 helix: 3.32 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.65 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP S 93 HIS 0.004 0.001 HIS K 128 PHE 0.023 0.003 PHE 4 41 TYR 0.022 0.003 TYR E 39 ARG 0.006 0.001 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.06287 ( 2710) hydrogen bonds : angle 3.99058 ( 8130) covalent geometry : bond 0.00364 (34776) covalent geometry : angle 0.65635 (46848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 4.424 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 2.0987 time to fit residues: 1099.0599 Evaluate side-chains 456 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 72 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 254 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 355 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 388 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 365 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 112 GLN 4 112 GLN 6 112 GLN A 112 GLN B 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN I 112 GLN K 112 GLN M 112 GLN O 112 GLN P 112 GLN Q 112 GLN S 112 GLN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN a 112 GLN e 112 GLN r 112 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.150172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.147615 restraints weight = 18595.327| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 0.17 r_work: 0.3331 rms_B_bonded: 0.64 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 1.33 restraints_weight: 0.2500 r_work: 0.3103 rms_B_bonded: 2.29 restraints_weight: 0.1250 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 34776 Z= 0.112 Angle : 0.521 5.603 46848 Z= 0.280 Chirality : 0.035 0.133 4920 Planarity : 0.003 0.024 6192 Dihedral : 4.230 20.386 4536 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.02 (0.13), residues: 4032 helix: 3.83 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.63 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 4 93 HIS 0.003 0.000 HIS X 128 PHE 0.012 0.002 PHE E 41 TYR 0.015 0.002 TYR W 39 ARG 0.002 0.000 ARG O 156 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 2710) hydrogen bonds : angle 3.54365 ( 8130) covalent geometry : bond 0.00209 (34776) covalent geometry : angle 0.52051 (46848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45193.49 seconds wall clock time: 783 minutes 39.69 seconds (47019.69 seconds total)