Starting phenix.real_space_refine on Thu Aug 8 00:46:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci2_16666/08_2024/8ci2_16666_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci2_16666/08_2024/8ci2_16666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci2_16666/08_2024/8ci2_16666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci2_16666/08_2024/8ci2_16666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci2_16666/08_2024/8ci2_16666_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci2_16666/08_2024/8ci2_16666_trim.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 7180 2.51 5 N 1874 2.21 5 O 2151 1.98 5 H 10298 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 156": "OD1" <-> "OD2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "I ASP 107": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21547 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3169 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3155 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3172 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3169 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "E" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3199 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "F" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1801 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1801 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "I" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1801 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.89, per 1000 atoms: 0.46 Number of scatterers: 21547 At special positions: 0 Unit cell: (93.12, 95.04, 119.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 2151 8.00 N 1874 7.00 C 7180 6.00 H 10298 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 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 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 401 " - " ASN A 23 " " NAG A 402 " - " ASN A 67 " " NAG B 401 " - " ASN B 23 " " NAG B 402 " - " ASN B 67 " " NAG C 401 " - " ASN C 23 " " NAG C 402 " - " ASN C 67 " " NAG D 401 " - " ASN D 23 " " NAG D 402 " - " ASN D 67 " " NAG E 401 " - " ASN E 23 " " NAG E 402 " - " ASN E 67 " Time building additional restraints: 16.29 Conformation dependent library (CDL) restraints added in 2.5 seconds 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 27 sheets defined 4.3% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.757A pdb=" N GLU C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.835A pdb=" N TYR I 33 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.631A pdb=" N LYS I 66 " --> pdb=" O SER I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.557A pdb=" N LEU A 108 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 59 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.557A pdb=" N LEU A 108 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 59 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.989A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.989A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 194 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.580A pdb=" N LEU B 108 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 59 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.580A pdb=" N LEU B 108 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 59 " --> pdb=" O CYS B 115 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.990A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.990A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.868A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP C 59 " --> pdb=" O CYS C 115 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 41 removed outlier: 5.169A pdb=" N LEU C 36 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP C 54 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 38 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR C 50 " --> pdb=" O MET C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 7.403A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 79 removed outlier: 3.537A pdb=" N TRP D 59 " --> pdb=" O CYS D 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 41 removed outlier: 7.038A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D 41 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.910A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 115 through 117 Processing sheet with id=AB8, first strand: chain 'E' and resid 115 through 117 removed outlier: 7.700A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.524A pdb=" N MET E 203 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.524A pdb=" N MET E 203 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 5 through 8 removed outlier: 3.608A pdb=" N VAL F 6 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA F 24 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 60 through 61 removed outlier: 6.030A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE F 52 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET F 35 " --> pdb=" O ILE F 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 19 through 22 Processing sheet with id=AC6, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.852A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR G 112 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.852A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 5 through 8 removed outlier: 3.885A pdb=" N SER I 22 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP I 74 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.607A pdb=" N PHE I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG I 39 " --> pdb=" O PHE I 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET I 35 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE I 38 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR I 96 " --> pdb=" O PHE I 38 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 885 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: 7.03 Time building geometry restraints manager: 17.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10290 1.03 - 1.23: 69 1.23 - 1.42: 5002 1.42 - 1.62: 6425 1.62 - 1.81: 71 Bond restraints: 21857 Sorted by residual: bond pdb=" CB PRO A 135 " pdb=" CG PRO A 135 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.80e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.27e+00 ... (remaining 21852 not shown) Histogram of bond angle deviations from ideal: 72.30 - 84.64: 3 84.64 - 96.98: 0 96.98 - 109.32: 13085 109.32 - 121.66: 21312 121.66 - 134.00: 4726 Bond angle restraints: 39126 Sorted by residual: angle pdb=" CB PHE C 134 " pdb=" CA PHE C 134 " pdb=" HA PHE C 134 " ideal model delta sigma weight residual 109.00 72.30 36.70 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C PHE C 134 " pdb=" CA PHE C 134 " pdb=" HA PHE C 134 " ideal model delta sigma weight residual 109.00 74.41 34.59 3.00e+00 1.11e-01 1.33e+02 angle pdb=" N PHE C 134 " pdb=" CA PHE C 134 " pdb=" HA PHE C 134 " ideal model delta sigma weight residual 110.00 76.86 33.14 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CA PRO A 135 " pdb=" N PRO A 135 " pdb=" CD PRO A 135 " ideal model delta sigma weight residual 112.00 101.23 10.77 1.40e+00 5.10e-01 5.92e+01 angle pdb=" CA LYS A 45 " pdb=" CB LYS A 45 " pdb=" CG LYS A 45 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 ... (remaining 39121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.70: 10019 25.70 - 51.39: 642 51.39 - 77.09: 88 77.09 - 102.78: 12 102.78 - 128.48: 2 Dihedral angle restraints: 10763 sinusoidal: 5773 harmonic: 4990 Sorted by residual: dihedral pdb=" CA TYR A 167 " pdb=" C TYR A 167 " pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta harmonic sigma weight residual 180.00 152.54 27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 47.18 45.82 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CA TYR B 167 " pdb=" C TYR B 167 " pdb=" N ILE B 168 " pdb=" CA ILE B 168 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 10760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1504 0.067 - 0.134: 208 0.134 - 0.201: 6 0.201 - 0.268: 0 0.268 - 0.335: 2 Chirality restraints: 1720 Sorted by residual: chirality pdb=" CA PHE C 134 " pdb=" N PHE C 134 " pdb=" C PHE C 134 " pdb=" CB PHE C 134 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 67 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 23 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 1717 not shown) Planarity restraints: 3327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 134 " -0.090 5.00e-02 4.00e+02 1.28e-01 2.64e+01 pdb=" N PRO A 135 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 134 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO C 135 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 135 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 135 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 45 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C LYS A 45 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS A 45 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A 46 " 0.013 2.00e-02 2.50e+03 ... (remaining 3324 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1757 2.21 - 2.81: 42255 2.81 - 3.41: 48373 3.41 - 4.00: 68116 4.00 - 4.60: 102456 Nonbonded interactions: 262957 Sorted by model distance: nonbonded pdb="HH21 ARG I 73 " pdb=" OD1 ASN I 75 " model vdw 1.617 2.450 nonbonded pdb=" O CYS G 23 " pdb=" HG1 THR G 79 " model vdw 1.623 2.450 nonbonded pdb=" HZ1 LYS C 144 " pdb=" OD2 ASP C 196 " model vdw 1.680 2.450 nonbonded pdb=" OD1 ASP C 196 " pdb=" H VAL C 197 " model vdw 1.703 2.450 nonbonded pdb=" OE1 GLU C 70 " pdb=" H GLU C 70 " model vdw 1.708 2.450 ... (remaining 262952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 195 through 206 or resi \ d 401 through 402)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 184 or (resid 185 through 192 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 193 through \ 206 or resid 401 through 402)) selection = (chain 'D' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 195 through 206 or resi \ d 401 through 402)) selection = (chain 'E' and (resid 1 through 184 or (resid 185 through 192 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 193 or (res \ id 194 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 195 through 206 or resid 401 through 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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 group one per residue 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: 0.450 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: 0.330 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 65.370 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.005 0.130 11559 Z= 0.318 Angle : 0.618 10.772 15742 Z= 0.309 Chirality : 0.045 0.335 1720 Planarity : 0.005 0.128 2003 Dihedral : 16.540 128.480 4403 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.89 % Favored : 85.11 % Rotamer: Outliers : 0.00 % Allowed : 17.70 % Favored : 82.30 % 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: -3.01 (0.21), residues: 1377 helix: 0.64 (0.78), residues: 45 sheet: -0.22 (0.23), residues: 505 loop : -3.58 (0.17), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 59 HIS 0.003 0.001 HIS B 114 PHE 0.010 0.001 PHE G 48 TYR 0.011 0.001 TYR E 14 ARG 0.003 0.000 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.834 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7986 (tt) cc_final: 0.7783 (tt) REVERT: A 98 ARG cc_start: 0.8055 (mtm180) cc_final: 0.6623 (mtm110) REVERT: B 124 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7721 (ttmt) REVERT: C 10 LEU cc_start: 0.8711 (tp) cc_final: 0.8510 (tp) REVERT: D 53 ILE cc_start: 0.8335 (mt) cc_final: 0.8081 (mt) REVERT: E 159 MET cc_start: 0.8538 (ttp) cc_final: 0.8004 (tmm) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.6117 time to fit residues: 213.5299 Evaluate side-chains 143 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11559 Z= 0.309 Angle : 0.630 5.569 15742 Z= 0.319 Chirality : 0.043 0.352 1720 Planarity : 0.006 0.083 2003 Dihedral : 9.688 115.996 1939 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.38 % Favored : 85.62 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -3.18 (0.20), residues: 1377 helix: -0.21 (0.76), residues: 45 sheet: -0.42 (0.23), residues: 505 loop : -3.58 (0.17), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 173 HIS 0.006 0.001 HIS A 140 PHE 0.015 0.001 PHE G 69 TYR 0.019 0.001 TYR A 167 ARG 0.018 0.001 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.562 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7494 (tt) cc_final: 0.7211 (tt) REVERT: A 98 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7054 (mtm110) REVERT: E 159 MET cc_start: 0.8402 (ttp) cc_final: 0.7918 (tmm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.6394 time to fit residues: 157.4667 Evaluate side-chains 128 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11559 Z= 0.269 Angle : 0.584 6.232 15742 Z= 0.295 Chirality : 0.043 0.353 1720 Planarity : 0.005 0.065 2003 Dihedral : 9.624 111.849 1939 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -3.11 (0.21), residues: 1377 helix: -0.02 (0.78), residues: 45 sheet: -0.23 (0.24), residues: 472 loop : -3.53 (0.17), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 173 HIS 0.006 0.001 HIS C 140 PHE 0.011 0.001 PHE B 99 TYR 0.011 0.001 TYR C 128 ARG 0.007 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.690 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: A 49 LEU cc_start: 0.7569 (tt) cc_final: 0.7307 (tt) REVERT: E 159 MET cc_start: 0.8410 (ttp) cc_final: 0.7920 (tmm) REVERT: E 167 TYR cc_start: 0.6960 (t80) cc_final: 0.6754 (t80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.5757 time to fit residues: 120.7006 Evaluate side-chains 113 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: