Starting phenix.real_space_refine on Mon Jul 22 08:49:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt9_19483/07_2024/8rt9_19483.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt9_19483/07_2024/8rt9_19483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt9_19483/07_2024/8rt9_19483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt9_19483/07_2024/8rt9_19483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt9_19483/07_2024/8rt9_19483.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt9_19483/07_2024/8rt9_19483.cif" } resolution = 2.97 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= 0.007 sd= 0.033 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 60 5.16 5 C 11349 2.51 5 N 3083 2.21 5 O 3374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "F ARG 27": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 194": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G ARG 194": "NH1" <-> "NH2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H ARG 194": "NH1" <-> "NH2" Residue "I ARG 66": "NH1" <-> "NH2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "I ARG 194": "NH1" <-> "NH2" Residue "J ARG 27": "NH1" <-> "NH2" Residue "J ARG 66": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 194": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17866 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1963 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1963 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 1977 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1977 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1977 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1977 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 1977 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1977 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1977 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 10.32, per 1000 atoms: 0.58 Number of scatterers: 17866 At special positions: 0 Unit cell: (109.901, 107.767, 234.74, 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 60 16.00 O 3374 8.00 N 3083 7.00 C 11349 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.18 Conformation dependent library (CDL) restraints added in 3.5 seconds 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4310 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 29 through 65 removed outlier: 3.635A pdb=" N ALA A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.505A pdb=" N GLU A 81 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 83 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.748A pdb=" N SER A 93 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.783A pdb=" N GLY A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 163 Processing helix chain 'A' and resid 167 through 219 removed outlier: 3.529A pdb=" N ILE A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 65 removed outlier: 3.636A pdb=" N ALA B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.504A pdb=" N GLU B 81 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 83 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER B 93 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.783A pdb=" N GLY B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 165 removed outlier: 3.511A pdb=" N SER B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 219 removed outlier: 3.528A pdb=" N ILE B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 65 removed outlier: 3.635A pdb=" N ALA C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.504A pdb=" N GLU C 81 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 83 " --> pdb=" O ARG C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER C 93 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 4.015A pdb=" N GLY C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 163 removed outlier: 3.601A pdb=" N SER C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 219 removed outlier: 3.528A pdb=" N ILE C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 65 removed outlier: 3.634A pdb=" N ALA D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.504A pdb=" N GLU D 81 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 83 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER D 93 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.533A pdb=" N GLY D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 164 removed outlier: 3.689A pdb=" N SER D 163 " --> pdb=" O MET D 159 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 219 removed outlier: 3.528A pdb=" N ILE D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 65 removed outlier: 3.635A pdb=" N ALA E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.505A pdb=" N GLU E 81 " --> pdb=" O GLN E 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E 83 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER E 93 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.500A pdb=" N GLY E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 163 removed outlier: 3.716A pdb=" N SER E 163 " --> pdb=" O MET E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 219 removed outlier: 3.529A pdb=" N ILE E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 22 Processing helix chain 'F' and resid 22 through 53 Proline residue: F 34 - end of helix Processing helix chain 'F' and resid 61 through 80 Processing helix chain 'F' and resid 82 through 101 removed outlier: 3.734A pdb=" N GLU F 86 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Proline residue: F 95 - end of helix removed outlier: 3.948A pdb=" N SER F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 137 Processing helix chain 'F' and resid 141 through 185 Proline residue: F 181 - end of helix Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 189 through 191 No H-bonds generated for 'chain 'F' and resid 189 through 191' Processing helix chain 'F' and resid 192 through 231 removed outlier: 3.805A pdb=" N PHE F 196 " --> pdb=" O ATHR F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 271 removed outlier: 3.582A pdb=" N LEU F 260 " --> pdb=" O LEU F 256 " (cutoff:3.500A) Proline residue: F 261 - end of helix Processing helix chain 'G' and resid 5 through 20 Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.512A pdb=" N SER G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) Proline residue: G 34 - end of helix Processing helix chain 'G' and resid 61 through 79 Processing helix chain 'G' and resid 82 through 101 removed outlier: 3.794A pdb=" N GLU G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Proline residue: G 95 - end of helix removed outlier: 4.084A pdb=" N SER G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 101 " --> pdb=" O GLU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 137 Processing helix chain 'G' and resid 141 through 185 Proline residue: G 181 - end of helix Processing helix chain 'G' and resid 186 through 188 No H-bonds generated for 'chain 'G' and resid 186 through 188' Processing helix chain 'G' and resid 192 through 231 removed outlier: 3.793A pdb=" N PHE G 196 " --> pdb=" O ATHR G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 271 removed outlier: 3.589A pdb=" N LEU G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Proline residue: G 261 - end of helix Processing helix chain 'H' and resid 5 through 53 removed outlier: 4.556A pdb=" N ASP H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Proline residue: H 34 - end of helix Processing helix chain 'H' and resid 61 through 80 Processing helix chain 'H' and resid 82 through 101 removed outlier: 3.994A pdb=" N GLU H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Proline residue: H 95 - end of helix removed outlier: 4.029A pdb=" N SER H 100 " --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 137 Processing helix chain 'H' and resid 141 through 185 Proline residue: H 181 - end of helix Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 192 through 231 removed outlier: 3.811A pdb=" N PHE H 196 " --> pdb=" O ATHR H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 271 Proline residue: H 261 - end of helix Processing helix chain 'I' and resid 5 through 53 removed outlier: 3.806A pdb=" N THR I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Proline residue: I 34 - end of helix Processing helix chain 'I' and resid 61 through 79 Processing helix chain 'I' and resid 82 through 101 removed outlier: 4.014A pdb=" N GLU I 86 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Proline residue: I 95 - end of helix removed outlier: 3.936A pdb=" N SER I 100 " --> pdb=" O ASP I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 137 Processing helix chain 'I' and resid 141 through 186 Proline residue: I 181 - end of helix Processing helix chain 'I' and resid 187 through 191 removed outlier: 5.275A pdb=" N GLN I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Proline residue: I 191 - end of helix No H-bonds generated for 'chain 'I' and resid 187 through 191' Processing helix chain 'I' and resid 192 through 230 removed outlier: 3.950A pdb=" N PHE I 196 " --> pdb=" O ATHR I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 271 Proline residue: I 261 - end of helix Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 21 through 53 Proline residue: J 34 - end of helix Processing helix chain 'J' and resid 61 through 80 Processing helix chain 'J' and resid 82 through 101 removed outlier: 4.036A pdb=" N GLU J 86 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Proline residue: J 95 - end of helix removed outlier: 3.991A pdb=" N SER J 100 " --> pdb=" O ASP J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 137 Processing helix chain 'J' and resid 141 through 186 Proline residue: J 181 - end of helix Processing helix chain 'J' and resid 192 through 230 removed outlier: 3.975A pdb=" N PHE J 196 " --> pdb=" O ATHR J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 271 Proline residue: J 261 - end of helix 1597 hydrogen bonds defined for protein. 4761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.90 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4797 1.33 - 1.45: 3041 1.45 - 1.57: 10153 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 18106 Sorted by residual: bond pdb=" N PRO H 95 " pdb=" CD PRO H 95 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.07e+01 bond pdb=" N THR H 33 " pdb=" CA THR H 33 " ideal model delta sigma weight residual 1.459 1.498 -0.038 1.04e-02 9.25e+03 1.37e+01 bond pdb=" N ILE B 102 " pdb=" CA ILE B 102 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.09e+00 bond pdb=" N THR A 165 " pdb=" CA THR A 165 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 9.09e+00 bond pdb=" N SER H 100 " pdb=" CA SER H 100 " ideal model delta sigma weight residual 1.458 1.485 -0.027 9.00e-03 1.23e+04 9.05e+00 ... (remaining 18101 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.80: 289 106.80 - 113.65: 10139 113.65 - 120.50: 7788 120.50 - 127.36: 6221 127.36 - 134.21: 75 Bond angle restraints: 24512 Sorted by residual: angle pdb=" CA GLY B 71 " pdb=" C GLY B 71 " pdb=" O GLY B 71 " ideal model delta sigma weight residual 122.29 117.07 5.22 8.10e-01 1.52e+00 4.15e+01 angle pdb=" N GLY J 80 " pdb=" CA GLY J 80 " pdb=" C GLY J 80 " ideal model delta sigma weight residual 114.40 108.24 6.16 1.11e+00 8.12e-01 3.08e+01 angle pdb=" N GLY B 71 " pdb=" CA GLY B 71 " pdb=" C GLY B 71 " ideal model delta sigma weight residual 112.68 106.32 6.36 1.26e+00 6.30e-01 2.55e+01 angle pdb=" C THR I 19 " pdb=" N TYR I 20 " pdb=" CA TYR I 20 " ideal model delta sigma weight residual 121.71 114.87 6.84 1.39e+00 5.18e-01 2.42e+01 angle pdb=" N LEU H 102 " pdb=" CA LEU H 102 " pdb=" C LEU H 102 " ideal model delta sigma weight residual 114.12 107.30 6.82 1.39e+00 5.18e-01 2.41e+01 ... (remaining 24507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9984 17.70 - 35.41: 660 35.41 - 53.11: 107 53.11 - 70.81: 31 70.81 - 88.52: 13 Dihedral angle restraints: 10795 sinusoidal: 4040 harmonic: 6755 Sorted by residual: dihedral pdb=" CA GLY D 71 " pdb=" C GLY D 71 " pdb=" N ASP D 72 " pdb=" CA ASP D 72 " ideal model delta harmonic sigma weight residual 180.00 -143.85 -36.15 0 5.00e+00 4.00e-02 5.23e+01 dihedral pdb=" CA GLY E 71 " pdb=" C GLY E 71 " pdb=" N ASP E 72 " pdb=" CA ASP E 72 " ideal model delta harmonic sigma weight residual -180.00 -143.89 -36.11 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" CA GLY A 71 " pdb=" C GLY A 71 " pdb=" N ASP A 72 " pdb=" CA ASP A 72 " ideal model delta harmonic sigma weight residual -180.00 -143.91 -36.09 0 5.00e+00 4.00e-02 5.21e+01 ... (remaining 10792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2703 0.104 - 0.209: 162 0.209 - 0.313: 7 0.313 - 0.417: 1 0.417 - 0.521: 1 Chirality restraints: 2874 Sorted by residual: chirality pdb=" CA THR H 33 " pdb=" N THR H 33 " pdb=" C THR H 33 " pdb=" CB THR H 33 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" CA LEU H 82 " pdb=" N LEU H 82 " pdb=" C LEU H 82 " pdb=" CB LEU H 82 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA LEU J 82 " pdb=" N LEU J 82 " pdb=" C LEU J 82 " pdb=" CB LEU J 82 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2871 not shown) Planarity restraints: 3202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 68 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C ARG B 68 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG B 68 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 69 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 18 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C ALA H 18 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA H 18 " 0.015 2.00e-02 2.50e+03 pdb=" N THR H 19 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 18 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C ALA G 18 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA G 18 " 0.014 2.00e-02 2.50e+03 pdb=" N THR G 19 " 0.013 2.00e-02 2.50e+03 ... (remaining 3199 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 6669 2.88 - 3.38: 19560 3.38 - 3.89: 31039 3.89 - 4.39: 35013 4.39 - 4.90: 57982 Nonbonded interactions: 150263 Sorted by model distance: nonbonded pdb=" O ILE J 243 " pdb=" OG SER J 246 " model vdw 2.370 2.440 nonbonded pdb=" O GLU D 81 " pdb=" OH TYR D 99 " model vdw 2.390 2.440 nonbonded pdb=" O PRO F 34 " pdb=" OG SER F 37 " model vdw 2.394 2.440 nonbonded pdb=" OG SER A 220 " pdb=" OE1 GLU J 132 " model vdw 2.417 2.440 nonbonded pdb=" O ASN G 89 " pdb=" OG1 THR G 93 " model vdw 2.420 2.440 ... (remaining 150258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 156 through \ 273)) selection = (chain 'H' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 156 through \ 273)) selection = (chain 'I' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 156 through \ 273)) selection = (chain 'J' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 156 through \ 273)) } 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: 35.270 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 49.680 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.007 0.078 18106 Z= 0.472 Angle : 0.790 7.714 24512 Z= 0.543 Chirality : 0.053 0.521 2874 Planarity : 0.004 0.046 3202 Dihedral : 12.660 88.516 6485 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 2.55 (0.17), residues: 2375 helix: 2.52 (0.11), residues: 1905 sheet: None (None), residues: 0 loop : -2.06 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 199 HIS 0.001 0.000 HIS G 193 PHE 0.026 0.002 PHE F 213 TYR 0.018 0.002 TYR H 83 ARG 0.013 0.001 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 611 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 TYR cc_start: 0.9055 (t80) cc_final: 0.8759 (t80) REVERT: H 129 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7582 (mt-10) REVERT: H 221 MET cc_start: 0.8281 (tpt) cc_final: 0.8019 (tpt) REVERT: J 230 ASP cc_start: 0.7794 (t0) cc_final: 0.7539 (t0) outliers start: 0 outliers final: 2 residues processed: 611 average time/residue: 1.3402 time to fit residues: 908.2083 Evaluate side-chains 374 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 372 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN F 118 GLN G 11 ASN G 201 GLN H 11 ASN H 118 GLN H 198 GLN H 202 GLN H 237 GLN I 11 ASN I 15 GLN I 118 GLN I 198 GLN J 11 ASN J 118 GLN J 201 GLN J 202 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18106 Z= 0.245 Angle : 0.572 10.202 24512 Z= 0.306 Chirality : 0.039 0.197 2874 Planarity : 0.004 0.040 3202 Dihedral : 5.126 141.085 2591 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.25 % Allowed : 14.84 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 3.05 (0.17), residues: 2375 helix: 2.83 (0.11), residues: 1895 sheet: None (None), residues: 0 loop : -1.59 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 189 HIS 0.001 0.000 HIS G 193 PHE 0.031 0.001 PHE H 213 TYR 0.014 0.002 TYR F 83 ARG 0.007 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 440 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 MET cc_start: 0.7911 (mtm) cc_final: 0.7663 (mtm) REVERT: F 201 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: G 69 ARG cc_start: 0.8169 (ttt90) cc_final: 0.7910 (ttt180) REVERT: H 230 ASP cc_start: 0.7531 (t0) cc_final: 0.7287 (t0) REVERT: J 230 ASP cc_start: 0.7681 (t0) cc_final: 0.7481 (t0) outliers start: 75 outliers final: 20 residues processed: 479 average time/residue: 1.2366 time to fit residues: 662.5137 Evaluate side-chains 388 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 367 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 201 GLN Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 138 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 0.4980 chunk 66 optimal weight: 0.0470 chunk 177 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 230 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN C 150 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN F 15 GLN F 198 GLN G 11 ASN G 118 GLN G 201 GLN H 11 ASN H 118 GLN H 202 GLN H 237 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 15 GLN J 118 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18106 Z= 0.194 Angle : 0.541 9.932 24512 Z= 0.282 Chirality : 0.037 0.186 2874 Planarity : 0.003 0.031 3202 Dihedral : 3.978 27.182 2585 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.19 % Allowed : 17.73 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.17), residues: 2375 helix: 2.89 (0.11), residues: 1895 sheet: None (None), residues: 0 loop : -1.45 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 189 HIS 0.001 0.000 HIS H 193 PHE 0.023 0.001 PHE H 213 TYR 0.014 0.001 TYR F 83 ARG 0.011 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 434 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 TYR cc_start: 0.7785 (t80) cc_final: 0.7537 (t80) REVERT: E 159 MET cc_start: 0.7830 (mtm) cc_final: 0.7630 (mtm) REVERT: G 69 ARG cc_start: 0.8117 (ttt90) cc_final: 0.7913 (ttt180) REVERT: H 230 ASP cc_start: 0.7492 (t0) cc_final: 0.7254 (t0) REVERT: J 132 GLU cc_start: 0.7572 (tt0) cc_final: 0.7319 (tt0) REVERT: J 230 ASP cc_start: 0.7564 (t0) cc_final: 0.7291 (t0) outliers start: 74 outliers final: 31 residues processed: 475 average time/residue: 1.2596 time to fit residues: 672.4831 Evaluate side-chains 416 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 385 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 258 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 118 GLN H 11 ASN H 202 GLN H 237 GLN H 259 GLN I 11 ASN I 118 GLN I 198 GLN J 118 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18106 Z= 0.231 Angle : 0.542 9.472 24512 Z= 0.283 Chirality : 0.038 0.182 2874 Planarity : 0.003 0.026 3202 Dihedral : 3.879 26.291 2585 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.85 % Allowed : 20.34 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.17), residues: 2375 helix: 2.92 (0.11), residues: 1895 sheet: None (None), residues: 0 loop : -1.30 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 189 HIS 0.001 0.000 HIS H 193 PHE 0.018 0.001 PHE H 213 TYR 0.014 0.001 TYR F 83 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 405 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7319 (mtp) REVERT: D 99 TYR cc_start: 0.7790 (t80) cc_final: 0.7531 (t80) REVERT: G 69 ARG cc_start: 0.8132 (ttt90) cc_final: 0.7916 (ttt180) REVERT: I 230 ASP cc_start: 0.7584 (t0) cc_final: 0.7332 (t0) outliers start: 68 outliers final: 28 residues processed: 439 average time/residue: 1.2219 time to fit residues: 600.4639 Evaluate side-chains 407 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 378 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 258 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 97 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN F 15 GLN F 198 GLN G 11 ASN G 15 GLN G 118 GLN H 11 ASN H 202 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 11 ASN J 15 GLN J 118 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18106 Z= 0.250 Angle : 0.561 9.887 24512 Z= 0.292 Chirality : 0.038 0.222 2874 Planarity : 0.003 0.038 3202 Dihedral : 3.852 25.137 2585 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.31 % Allowed : 21.19 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.17), residues: 2375 helix: 2.90 (0.11), residues: 1895 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 189 HIS 0.001 0.000 HIS I 193 PHE 0.027 0.001 PHE B 36 TYR 0.016 0.001 TYR F 83 ARG 0.009 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 393 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 TYR cc_start: 0.7873 (t80) cc_final: 0.7651 (t80) REVERT: F 65 ASN cc_start: 0.8418 (p0) cc_final: 0.8123 (p0) REVERT: J 11 ASN cc_start: 0.8104 (m-40) cc_final: 0.7892 (m-40) outliers start: 76 outliers final: 36 residues processed: 431 average time/residue: 1.1745 time to fit residues: 570.2241 Evaluate side-chains 404 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 368 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 68 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 105 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 ASN F 11 ASN F 198 GLN G 11 ASN G 118 GLN H 11 ASN H 202 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 118 GLN J 259 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18106 Z= 0.210 Angle : 0.559 9.719 24512 Z= 0.292 Chirality : 0.038 0.183 2874 Planarity : 0.003 0.025 3202 Dihedral : 3.801 23.926 2585 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.36 % Allowed : 21.76 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.17), residues: 2375 helix: 2.94 (0.11), residues: 1890 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 189 HIS 0.001 0.000 HIS H 193 PHE 0.029 0.001 PHE H 213 TYR 0.018 0.001 TYR F 83 ARG 0.005 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 385 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8116 (tp40) REVERT: D 99 TYR cc_start: 0.7807 (t80) cc_final: 0.7573 (t80) REVERT: D 197 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: E 159 MET cc_start: 0.7551 (mtm) cc_final: 0.7312 (mtp) outliers start: 77 outliers final: 39 residues processed: 427 average time/residue: 1.1271 time to fit residues: 543.2082 Evaluate side-chains 409 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 368 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 213 PHE Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 185 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 129 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 0.0470 chunk 126 optimal weight: 0.5980 chunk 226 optimal weight: 0.4980 chunk 141 optimal weight: 0.8980 chunk 138 optimal weight: 0.0270 chunk 104 optimal weight: 10.0000 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 198 GLN G 11 ASN G 118 GLN H 11 ASN I 11 ASN I 118 GLN I 198 GLN J 118 GLN J 259 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18106 Z= 0.167 Angle : 0.554 10.074 24512 Z= 0.287 Chirality : 0.038 0.204 2874 Planarity : 0.003 0.026 3202 Dihedral : 3.760 21.478 2585 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.72 % Allowed : 23.57 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.17), residues: 2375 helix: 2.94 (0.11), residues: 1900 sheet: None (None), residues: 0 loop : -1.30 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP I 189 HIS 0.001 0.001 HIS H 193 PHE 0.028 0.001 PHE D 36 TYR 0.013 0.001 TYR F 83 ARG 0.004 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 418 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7881 (mmp) REVERT: C 197 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8052 (tp40) REVERT: D 99 TYR cc_start: 0.7706 (t80) cc_final: 0.7410 (t80) REVERT: G 132 GLU cc_start: 0.7419 (tt0) cc_final: 0.7110 (mt-10) REVERT: I 230 ASP cc_start: 0.7399 (t0) cc_final: 0.7165 (t0) outliers start: 48 outliers final: 24 residues processed: 448 average time/residue: 1.1055 time to fit residues: 564.6782 Evaluate side-chains 406 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 380 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 213 PHE Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 185 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN G 11 ASN G 118 GLN G 198 GLN H 11 ASN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 118 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18106 Z= 0.228 Angle : 0.606 10.440 24512 Z= 0.312 Chirality : 0.039 0.207 2874 Planarity : 0.003 0.047 3202 Dihedral : 3.704 22.061 2585 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.78 % Allowed : 24.99 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.17), residues: 2375 helix: 2.91 (0.11), residues: 1910 sheet: None (None), residues: 0 loop : -1.51 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 189 HIS 0.001 0.000 HIS J 193 PHE 0.031 0.002 PHE C 36 TYR 0.014 0.001 TYR F 227 ARG 0.011 0.000 ARG H 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 384 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8083 (tp40) REVERT: D 99 TYR cc_start: 0.7748 (t80) cc_final: 0.7471 (t80) REVERT: I 230 ASP cc_start: 0.7483 (t0) cc_final: 0.7255 (t0) outliers start: 49 outliers final: 31 residues processed: 417 average time/residue: 1.1284 time to fit residues: 531.4276 Evaluate side-chains 404 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 372 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 213 PHE Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 185 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 211 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 199 optimal weight: 0.0020 chunk 210 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 198 GLN G 11 ASN G 198 GLN H 11 ASN H 259 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 118 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18106 Z= 0.212 Angle : 0.614 10.997 24512 Z= 0.314 Chirality : 0.039 0.208 2874 Planarity : 0.003 0.048 3202 Dihedral : 3.748 25.990 2585 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.55 % Allowed : 25.16 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.17), residues: 2375 helix: 2.83 (0.11), residues: 1920 sheet: None (None), residues: 0 loop : -1.49 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 189 HIS 0.001 0.000 HIS J 193 PHE 0.034 0.002 PHE E 36 TYR 0.019 0.001 TYR H 83 ARG 0.010 0.000 ARG H 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 379 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8070 (tp40) REVERT: D 99 TYR cc_start: 0.7730 (t80) cc_final: 0.7434 (t80) REVERT: G 132 GLU cc_start: 0.7422 (tt0) cc_final: 0.7112 (mt-10) REVERT: I 230 ASP cc_start: 0.7451 (t0) cc_final: 0.7219 (t0) outliers start: 45 outliers final: 30 residues processed: 406 average time/residue: 1.1045 time to fit residues: 507.5333 Evaluate side-chains 402 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 371 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 213 PHE Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 chunk 136 optimal weight: 0.0670 chunk 105 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 215 optimal weight: 0.4980 chunk 186 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN G 11 ASN G 198 GLN H 11 ASN H 259 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 118 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18106 Z= 0.206 Angle : 0.631 12.050 24512 Z= 0.320 Chirality : 0.039 0.211 2874 Planarity : 0.003 0.045 3202 Dihedral : 3.734 26.948 2585 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.15 % Allowed : 25.50 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.17), residues: 2375 helix: 2.80 (0.11), residues: 1920 sheet: None (None), residues: 0 loop : -1.48 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 189 HIS 0.001 0.000 HIS H 193 PHE 0.032 0.002 PHE E 36 TYR 0.017 0.001 TYR H 83 ARG 0.010 0.000 ARG H 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 386 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8092 (tp40) REVERT: D 99 TYR cc_start: 0.7711 (t80) cc_final: 0.7434 (t80) REVERT: G 132 GLU cc_start: 0.7441 (tt0) cc_final: 0.7118 (mt-10) REVERT: I 230 ASP cc_start: 0.7429 (t0) cc_final: 0.7199 (t0) outliers start: 38 outliers final: 25 residues processed: 410 average time/residue: 1.1442 time to fit residues: 530.6063 Evaluate side-chains 402 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 376 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 213 PHE Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 191 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 118 GLN F 198 GLN G 11 ASN G 118 GLN G 198 GLN H 259 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 118 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.063830 restraints weight = 40450.142| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.64 r_work: 0.2820 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18106 Z= 0.226 Angle : 0.636 10.549 24512 Z= 0.324 Chirality : 0.039 0.204 2874 Planarity : 0.003 0.044 3202 Dihedral : 3.742 30.012 2585 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.32 % Allowed : 25.84 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 3.05 (0.17), residues: 2375 helix: 2.77 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -1.53 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 189 HIS 0.001 0.000 HIS J 193 PHE 0.032 0.002 PHE A 36 TYR 0.018 0.001 TYR F 227 ARG 0.009 0.000 ARG H 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8655.35 seconds wall clock time: 151 minutes 32.83 seconds (9092.83 seconds total)