Starting phenix.real_space_refine on Tue Jun 10 21:20:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rq5_19434/06_2025/8rq5_19434.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rq5_19434/06_2025/8rq5_19434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rq5_19434/06_2025/8rq5_19434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rq5_19434/06_2025/8rq5_19434.map" model { file = "/net/cci-nas-00/data/ceres_data/8rq5_19434/06_2025/8rq5_19434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rq5_19434/06_2025/8rq5_19434.cif" } resolution = 2.32 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= 0.001 sd= 0.065 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 45 5.16 5 Na 5 4.78 5 C 8191 2.51 5 N 1628 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12137 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2157 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 268, 2117 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 268, 2117 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2128 Chain: "B" Number of atoms: 2159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 268, 2119 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 268, 2119 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2130 Chain: "C" Number of atoms: 2160 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 268, 2120 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 268, 2120 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2131 Chain: "D" Number of atoms: 2154 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 268, 2120 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 268, 2120 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2138 Chain: "E" Number of atoms: 2154 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 268, 2120 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 268, 2120 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 262} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2138 Chain: "A" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 181 Unusual residues: {' NA': 1, 'LFA': 12, 'OLA': 1, 'OLC': 1, 'RET': 1} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'OLC:plan-2': 1, 'RET:plan-5': 1, 'OLC:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 185 Unusual residues: {' NA': 1, 'LFA': 13, 'OLA': 1, 'OLC': 1, 'RET': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'OLC:plan-2': 1, 'RET:plan-5': 1, 'OLC:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 231 Unusual residues: {' NA': 1, 'LFA': 14, 'OLC': 2, 'RET': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 207 Unusual residues: {' NA': 1, 'LFA': 14, 'OLA': 1, 'OLC': 1, 'RET': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'OLC:plan-2': 1, 'RET:plan-5': 1, 'OLC:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 197 Unusual residues: {' NA': 1, 'LFA': 13, 'OLA': 1, 'RET': 1} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N ASER A 29 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 29 " occ=0.50 residue: pdb=" N AGLN A 78 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 78 " occ=0.50 residue: pdb=" N APHE A 179 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 179 " occ=0.50 residue: pdb=" N ATRP A 183 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 183 " occ=0.50 residue: pdb=" N ASER B 29 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 29 " occ=0.50 residue: pdb=" N AGLN B 78 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN B 78 " occ=0.40 residue: pdb=" N APHE B 179 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 179 " occ=0.50 residue: pdb=" N ATRP B 183 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP B 183 " occ=0.50 residue: pdb=" N ASER C 29 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 29 " occ=0.50 residue: pdb=" N AGLN C 78 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 78 " occ=0.50 residue: pdb=" N APHE C 179 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 179 " occ=0.50 residue: pdb=" N ATRP C 183 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP C 183 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 12.57, per 1000 atoms: 1.04 Number of scatterers: 12137 At special positions: 0 Unit cell: (97.324, 96.485, 76.349, 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 45 16.00 Na 5 11.00 O 2268 8.00 N 1628 7.00 C 8191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 2.8 seconds 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 5 sheets defined 82.8% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.960A pdb=" N PHE A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 49 Processing helix chain 'A' and resid 50 through 53 removed outlier: 3.511A pdb=" N VAL A 53 " --> pdb=" O ILE A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 50 through 53' Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 57 through 85 removed outlier: 3.975A pdb=" N ASN A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 106 through 125 removed outlier: 3.775A pdb=" N TYR A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Proline residue: A 118 - end of helix removed outlier: 4.056A pdb=" N ILE A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 158 removed outlier: 4.032A pdb=" N PHE A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 194 removed outlier: 3.599A pdb=" N GLU A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 224 removed outlier: 4.136A pdb=" N TYR A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 236 through 270 removed outlier: 3.653A pdb=" N ILE A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 18 removed outlier: 3.956A pdb=" N PHE B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 49 Processing helix chain 'B' and resid 50 through 53 removed outlier: 3.515A pdb=" N VAL B 53 " --> pdb=" O ILE B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 53' Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 57 through 85 removed outlier: 3.974A pdb=" N ASN B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 106 through 125 removed outlier: 3.781A pdb=" N TYR B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 114 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Proline residue: B 118 - end of helix removed outlier: 4.052A pdb=" N ILE B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 removed outlier: 4.037A pdb=" N PHE B 158 " --> pdb=" O TYR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 194 removed outlier: 3.603A pdb=" N GLU B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 224 removed outlier: 4.142A pdb=" N TYR B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 236 through 270 removed outlier: 3.652A pdb=" N ILE B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.953A pdb=" N PHE C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 49 Processing helix chain 'C' and resid 50 through 53 removed outlier: 3.511A pdb=" N VAL C 53 " --> pdb=" O ILE C 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 53' Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 57 through 85 removed outlier: 3.967A pdb=" N ASN C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 106 through 125 removed outlier: 3.777A pdb=" N TYR C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 114 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Proline residue: C 118 - end of helix removed outlier: 4.050A pdb=" N ILE C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 158 removed outlier: 4.039A pdb=" N PHE C 158 " --> pdb=" O TYR C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 194 removed outlier: 3.615A pdb=" N GLU C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 224 removed outlier: 4.141A pdb=" N TYR C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 236 through 270 removed outlier: 3.648A pdb=" N ILE C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 18 removed outlier: 3.954A pdb=" N PHE D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 49 Processing helix chain 'D' and resid 50 through 53 removed outlier: 3.533A pdb=" N VAL D 53 " --> pdb=" O ILE D 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 50 through 53' Processing helix chain 'D' and resid 54 through 56 No H-bonds generated for 'chain 'D' and resid 54 through 56' Processing helix chain 'D' and resid 57 through 85 removed outlier: 3.970A pdb=" N ASN D 61 " --> pdb=" O PHE D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.770A pdb=" N TYR D 110 " --> pdb=" O ASN D 106 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 114 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Proline residue: D 118 - end of helix removed outlier: 4.049A pdb=" N ILE D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 158 removed outlier: 4.030A pdb=" N PHE D 158 " --> pdb=" O TYR D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 194 removed outlier: 3.592A pdb=" N GLU D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 224 removed outlier: 4.145A pdb=" N TYR D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Proline residue: D 219 - end of helix Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 236 through 270 removed outlier: 3.651A pdb=" N ILE D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 18 removed outlier: 3.950A pdb=" N PHE E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 49 Processing helix chain 'E' and resid 50 through 53 removed outlier: 3.517A pdb=" N VAL E 53 " --> pdb=" O ILE E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 50 through 53' Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 57 through 85 removed outlier: 3.983A pdb=" N ASN E 61 " --> pdb=" O PHE E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 102 Processing helix chain 'E' and resid 106 through 125 removed outlier: 3.773A pdb=" N TYR E 110 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 114 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Proline residue: E 118 - end of helix removed outlier: 4.050A pdb=" N ILE E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 158 removed outlier: 4.031A pdb=" N PHE E 158 " --> pdb=" O TYR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 193 Processing helix chain 'E' and resid 197 through 224 removed outlier: 4.137A pdb=" N TYR E 218 " --> pdb=" O SER E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 236 through 270 removed outlier: 3.652A pdb=" N ILE E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 89 removed outlier: 3.585A pdb=" N ARG A 94 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 89 removed outlier: 3.578A pdb=" N ARG B 94 " --> pdb=" O ASN B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 86 through 89 removed outlier: 3.582A pdb=" N ARG C 94 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 86 through 89 removed outlier: 3.587A pdb=" N ARG D 94 " --> pdb=" O ASN D 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 86 through 89 removed outlier: 3.577A pdb=" N ARG E 94 " --> pdb=" O ASN E 89 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2526 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: 3.67 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2694 1.33 - 1.47: 3860 1.47 - 1.60: 5384 1.60 - 1.73: 0 1.73 - 1.86: 90 Bond restraints: 12028 Sorted by residual: bond pdb=" C7 LFA D 306 " pdb=" C8 LFA D 306 " ideal model delta sigma weight residual 1.524 1.426 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C1 OLA A 305 " pdb=" O1 OLA A 305 " ideal model delta sigma weight residual 1.248 1.335 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 OLA D 301 " pdb=" O1 OLA D 301 " ideal model delta sigma weight residual 1.248 1.331 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C10 RET B 304 " pdb=" C11 RET B 304 " ideal model delta sigma weight residual 1.433 1.354 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C6 LFA E 312 " pdb=" C7 LFA E 312 " ideal model delta sigma weight residual 1.524 1.445 0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 12023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 13010 1.68 - 3.36: 2629 3.36 - 5.04: 321 5.04 - 6.72: 68 6.72 - 8.39: 14 Bond angle restraints: 16042 Sorted by residual: angle pdb=" CA HIS A 180 " pdb=" CB HIS A 180 " pdb=" CG HIS A 180 " ideal model delta sigma weight residual 113.80 108.46 5.34 1.00e+00 1.00e+00 2.85e+01 angle pdb=" CA HIS B 180 " pdb=" CB HIS B 180 " pdb=" CG HIS B 180 " ideal model delta sigma weight residual 113.80 108.78 5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" CA HIS E 180 " pdb=" CB HIS E 180 " pdb=" CG HIS E 180 " ideal model delta sigma weight residual 113.80 108.83 4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" CA HIS D 180 " pdb=" CB HIS D 180 " pdb=" CG HIS D 180 " ideal model delta sigma weight residual 113.80 108.99 4.81 1.00e+00 1.00e+00 2.31e+01 angle pdb=" CA HIS C 180 " pdb=" CB HIS C 180 " pdb=" CG HIS C 180 " ideal model delta sigma weight residual 113.80 109.01 4.79 1.00e+00 1.00e+00 2.29e+01 ... (remaining 16037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 6796 35.52 - 71.04: 149 71.04 - 106.57: 3 106.57 - 142.09: 0 142.09 - 177.61: 2 Dihedral angle restraints: 6950 sinusoidal: 2998 harmonic: 3952 Sorted by residual: dihedral pdb=" C21 OLC C 306 " pdb=" C22 OLC C 306 " pdb=" C24 OLC C 306 " pdb=" O25 OLC C 306 " ideal model delta sinusoidal sigma weight residual -174.20 3.41 -177.61 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O23 OLC C 306 " pdb=" C22 OLC C 306 " pdb=" C24 OLC C 306 " pdb=" O25 OLC C 306 " ideal model delta sinusoidal sigma weight residual 60.48 -122.12 -177.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N SER A 236 " pdb=" CA SER A 236 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 6947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 976 0.060 - 0.121: 512 0.121 - 0.181: 158 0.181 - 0.241: 43 0.241 - 0.302: 16 Chirality restraints: 1705 Sorted by residual: chirality pdb=" CA GLN A 123 " pdb=" N GLN A 123 " pdb=" C GLN A 123 " pdb=" CB GLN A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA GLN B 123 " pdb=" N GLN B 123 " pdb=" C GLN B 123 " pdb=" CB GLN B 123 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA GLN C 123 " pdb=" N GLN C 123 " pdb=" C GLN C 123 " pdb=" CB GLN C 123 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1702 not shown) Planarity restraints: 1897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA D 301 " -0.133 2.00e-02 2.50e+03 1.27e-01 1.60e+02 pdb=" C11 OLA D 301 " 0.128 2.00e-02 2.50e+03 pdb=" C8 OLA D 301 " 0.125 2.00e-02 2.50e+03 pdb=" C9 OLA D 301 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET E 305 " 0.079 2.00e-02 2.50e+03 9.73e-02 1.18e+02 pdb=" C13 RET E 305 " -0.006 2.00e-02 2.50e+03 pdb=" C14 RET E 305 " -0.166 2.00e-02 2.50e+03 pdb=" C15 RET E 305 " 0.115 2.00e-02 2.50e+03 pdb=" C20 RET E 305 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET B 304 " -0.078 2.00e-02 2.50e+03 9.62e-02 1.16e+02 pdb=" C13 RET B 304 " 0.007 2.00e-02 2.50e+03 pdb=" C14 RET B 304 " 0.164 2.00e-02 2.50e+03 pdb=" C15 RET B 304 " -0.113 2.00e-02 2.50e+03 pdb=" C20 RET B 304 " 0.021 2.00e-02 2.50e+03 ... (remaining 1894 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3548 2.81 - 3.33: 12037 3.33 - 3.85: 22745 3.85 - 4.38: 29277 4.38 - 4.90: 45747 Nonbonded interactions: 113354 Sorted by model distance: nonbonded pdb=" O HOH E 417 " pdb=" O HOH E 423 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR E 248 " pdb=" O HOH E 401 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR B 248 " pdb=" O HOH B 401 " model vdw 2.318 3.040 nonbonded pdb=" O TYR A 25 " pdb=" OG BSER A 29 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR D 248 " pdb=" O HOH D 401 " model vdw 2.341 3.040 ... (remaining 113349 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 3 through 28 or resid 30 through 77 or resid 79 through 11 \ 3 or (resid 114 and (name N or name CA or name C or name CB or name CG or name C \ D1 or name CD2)) or resid 115 through 178 or resid 180 through 182 or resid 184 \ through 270 or (resid 302 and (name C1 or name C10 or name C11 or name C2 or nam \ e C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (re \ sid 315 and (name C8 )))) selection = (chain 'B' and (resid 3 through 28 or resid 30 through 55 or (resid 56 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or resid 5 \ 7 through 77 or resid 79 through 178 or resid 180 through 182 or resid 184 throu \ gh 186 or (resid 187 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name CE )) or resid 188 through 270 or (resid 302 and (name \ C1 or name C10 or name C11 or name C2 or name C3 or name C4 or name C5 or name C \ 6 or name C7 or name C8 or name C9 )) or (resid 315 and (name C8 )))) selection = (chain 'C' and (resid 3 through 28 or resid 30 through 55 or (resid 56 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or resid 5 \ 7 through 77 or resid 79 through 113 or (resid 114 and (name N or name CA or nam \ e C or name CB or name CG or name CD1 or name CD2)) or resid 115 through 178 or \ resid 180 through 182 or resid 184 through 201 or (resid 202 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 203 through 270 or (re \ sid 302 and (name C1 or name C10 or name C11 or name C2 or name C3 or name C4 or \ name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 315 and (name \ C8 )))) selection = (chain 'D' and (resid 3 through 28 or resid 30 through 55 or (resid 56 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or resid 5 \ 7 through 77 or resid 79 through 113 or (resid 114 and (name N or name CA or nam \ e C or name CB or name CG or name CD1 or name CD2)) or resid 115 through 178 or \ resid 180 through 182 or resid 184 through 201 or (resid 202 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 203 through 270 or (re \ sid 302 and (name C1 or name C10 or name C11 or name C2 or name C3 or name C4 or \ name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 315 and (name \ C8 )))) selection = (chain 'E' and (resid 3 through 28 or resid 30 through 55 or (resid 56 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or resid 5 \ 7 through 77 or resid 79 through 113 or (resid 114 and (name N or name CA or nam \ e C or name CB or name CG or name CD1 or name CD2)) or resid 115 through 178 or \ resid 180 through 182 or resid 184 through 201 or (resid 202 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 203 through 270 or res \ id 302 or (resid 315 and (name C8 )))) } 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=0.40 max=1.00 mean=0.98 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: 1.960 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.420 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 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 : 0.012 0.166 12033 Z= 0.806 Angle : 1.375 8.394 16042 Z= 0.918 Chirality : 0.082 0.302 1705 Planarity : 0.013 0.127 1897 Dihedral : 14.563 177.608 4444 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.01 % Allowed : 4.70 % Favored : 92.29 % 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: -0.73 (0.19), residues: 1384 helix: -0.43 (0.13), residues: 1015 sheet: -2.28 (0.60), residues: 40 loop : 0.23 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.014 TRP E 82 HIS 0.007 0.003 HIS C 30 PHE 0.047 0.012 PHE C 27 TYR 0.044 0.010 TYR D 258 ARG 0.035 0.008 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.19610 ( 841) hydrogen bonds : angle 6.48932 ( 2526) covalent geometry : bond 0.01204 (12028) covalent geometry : angle 1.37466 (16042) Misc. bond : bond 0.16504 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.225 Fit side-chains REVERT: A 185 MET cc_start: 0.9157 (tpp) cc_final: 0.8760 (tpp) REVERT: B 90 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: D 90 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: D 119 MET cc_start: 0.9032 (mmp) cc_final: 0.8799 (mmp) REVERT: D 224 MET cc_start: 0.9158 (tpp) cc_final: 0.8773 (tpp) REVERT: E 68 MET cc_start: 0.9266 (mmp) cc_final: 0.8839 (mmp) REVERT: E 90 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7556 (pm20) outliers start: 33 outliers final: 7 residues processed: 160 average time/residue: 1.2609 time to fit residues: 219.8961 Evaluate side-chains 134 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 112 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 112 ASN C 112 ASN C 163 ASN C 180 HIS D 112 ASN D 180 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.079637 restraints weight = 79916.080| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.60 r_work: 0.2654 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12033 Z= 0.143 Angle : 0.514 5.448 16042 Z= 0.296 Chirality : 0.038 0.122 1705 Planarity : 0.004 0.022 1897 Dihedral : 11.475 167.838 2199 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.22 % Allowed : 7.09 % Favored : 90.69 % 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: 2.90 (0.21), residues: 1384 helix: 2.32 (0.14), residues: 1069 sheet: None (None), residues: 0 loop : 0.63 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 215 HIS 0.005 0.002 HIS A 180 PHE 0.016 0.002 PHE D 27 TYR 0.022 0.002 TYR C 36 ARG 0.002 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.06741 ( 841) hydrogen bonds : angle 4.02626 ( 2526) covalent geometry : bond 0.00263 (12028) covalent geometry : angle 0.51437 (16042) Misc. bond : bond 0.00035 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.142 Fit side-chains REVERT: A 185 MET cc_start: 0.9210 (tpp) cc_final: 0.8867 (tpp) REVERT: B 90 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6949 (pm20) REVERT: C 22 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: D 68 MET cc_start: 0.9333 (mmp) cc_final: 0.8976 (mmp) REVERT: D 90 GLU cc_start: 0.8266 (pt0) cc_final: 0.7081 (pm20) REVERT: E 39 MET cc_start: 0.9305 (mmt) cc_final: 0.8683 (mmt) REVERT: E 68 MET cc_start: 0.9339 (mmp) cc_final: 0.8986 (mmp) REVERT: E 90 GLU cc_start: 0.8425 (pt0) cc_final: 0.7175 (pm20) outliers start: 24 outliers final: 8 residues processed: 147 average time/residue: 1.2730 time to fit residues: 203.1283 Evaluate side-chains 135 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 180 HIS B 112 ASN B 180 HIS C 112 ASN D 112 ASN E 180 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.080896 restraints weight = 81556.437| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.88 r_work: 0.2668 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 12033 Z= 0.138 Angle : 0.486 5.599 16042 Z= 0.277 Chirality : 0.038 0.130 1705 Planarity : 0.003 0.025 1897 Dihedral : 10.585 119.234 2184 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.86 % Allowed : 7.80 % Favored : 90.34 % 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: 3.37 (0.21), residues: 1384 helix: 2.68 (0.15), residues: 1069 sheet: None (None), residues: 0 loop : 0.68 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 215 HIS 0.005 0.002 HIS A 180 PHE 0.016 0.002 PHE D 27 TYR 0.024 0.002 TYR C 36 ARG 0.002 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.06178 ( 841) hydrogen bonds : angle 3.85930 ( 2526) covalent geometry : bond 0.00266 (12028) covalent geometry : angle 0.48557 (16042) Misc. bond : bond 0.00054 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.312 Fit side-chains REVERT: A 185 MET cc_start: 0.9177 (tpp) cc_final: 0.8798 (tpp) REVERT: B 90 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7082 (pm20) REVERT: C 22 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: D 90 GLU cc_start: 0.8316 (pt0) cc_final: 0.7146 (pm20) REVERT: E 68 MET cc_start: 0.9314 (mmp) cc_final: 0.9009 (mmp) REVERT: E 90 GLU cc_start: 0.8429 (pt0) cc_final: 0.7278 (pm20) outliers start: 20 outliers final: 9 residues processed: 151 average time/residue: 1.3382 time to fit residues: 219.6029 Evaluate side-chains 143 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 8 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 80 GLN B 112 ASN C 112 ASN D 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.098847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.079490 restraints weight = 83610.898| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.58 r_work: 0.2634 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12033 Z= 0.162 Angle : 0.511 5.817 16042 Z= 0.290 Chirality : 0.040 0.135 1705 Planarity : 0.004 0.027 1897 Dihedral : 10.955 97.910 2184 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.04 % Allowed : 8.24 % Favored : 89.72 % 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 (0.22), residues: 1384 helix: 2.65 (0.15), residues: 1064 sheet: -2.58 (0.56), residues: 50 loop : 0.62 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.004 0.002 HIS E 180 PHE 0.018 0.002 PHE B 27 TYR 0.024 0.002 TYR C 36 ARG 0.002 0.000 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.06678 ( 841) hydrogen bonds : angle 3.89188 ( 2526) covalent geometry : bond 0.00337 (12028) covalent geometry : angle 0.51112 (16042) Misc. bond : bond 0.00087 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.267 Fit side-chains REVERT: A 185 MET cc_start: 0.9183 (tpp) cc_final: 0.8794 (tpp) REVERT: B 90 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: C 22 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: C 241 MET cc_start: 0.9144 (mtp) cc_final: 0.8840 (mtm) REVERT: D 90 GLU cc_start: 0.8352 (pt0) cc_final: 0.7358 (pm20) REVERT: E 68 MET cc_start: 0.9298 (mmp) cc_final: 0.9073 (mmp) REVERT: E 90 GLU cc_start: 0.8478 (pt0) cc_final: 0.7297 (pm20) outliers start: 22 outliers final: 11 residues processed: 152 average time/residue: 1.1481 time to fit residues: 190.9041 Evaluate side-chains 147 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 112 ASN C 112 ASN D 112 ASN E 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.079823 restraints weight = 79212.857| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.56 r_work: 0.2647 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12033 Z= 0.157 Angle : 0.503 6.593 16042 Z= 0.285 Chirality : 0.039 0.135 1705 Planarity : 0.004 0.027 1897 Dihedral : 11.020 72.663 2184 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.04 % Allowed : 8.16 % Favored : 89.80 % 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: 3.09 (0.22), residues: 1384 helix: 2.63 (0.15), residues: 1064 sheet: -2.58 (0.57), residues: 50 loop : 0.63 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.003 0.001 HIS C 180 PHE 0.016 0.002 PHE B 27 TYR 0.024 0.002 TYR C 36 ARG 0.002 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.06537 ( 841) hydrogen bonds : angle 3.87669 ( 2526) covalent geometry : bond 0.00322 (12028) covalent geometry : angle 0.50253 (16042) Misc. bond : bond 0.00079 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.238 Fit side-chains REVERT: A 185 MET cc_start: 0.9129 (tpp) cc_final: 0.8785 (tpp) REVERT: B 90 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: C 22 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: C 241 MET cc_start: 0.9143 (mtp) cc_final: 0.8840 (mtm) REVERT: D 90 GLU cc_start: 0.8392 (pt0) cc_final: 0.7385 (pm20) REVERT: E 68 MET cc_start: 0.9288 (mmp) cc_final: 0.9079 (mmp) REVERT: E 90 GLU cc_start: 0.8546 (pt0) cc_final: 0.7379 (pm20) outliers start: 22 outliers final: 11 residues processed: 153 average time/residue: 1.2563 time to fit residues: 209.4611 Evaluate side-chains 145 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 36 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 112 ASN C 112 ASN D 112 ASN E 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.101987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.082896 restraints weight = 76344.893| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.82 r_work: 0.2697 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12033 Z= 0.123 Angle : 0.457 7.326 16042 Z= 0.258 Chirality : 0.037 0.126 1705 Planarity : 0.003 0.027 1897 Dihedral : 10.180 59.641 2184 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.60 % Allowed : 9.04 % Favored : 89.36 % 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: 3.53 (0.22), residues: 1384 helix: 2.79 (0.15), residues: 1069 sheet: None (None), residues: 0 loop : 0.72 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 208 HIS 0.003 0.001 HIS B 180 PHE 0.013 0.002 PHE D 167 TYR 0.024 0.001 TYR C 36 ARG 0.001 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.05698 ( 841) hydrogen bonds : angle 3.77159 ( 2526) covalent geometry : bond 0.00228 (12028) covalent geometry : angle 0.45686 (16042) Misc. bond : bond 0.00033 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: B 90 GLU cc_start: 0.8444 (pt0) cc_final: 0.7293 (pm20) REVERT: C 22 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: C 241 MET cc_start: 0.9098 (mtp) cc_final: 0.8790 (mtm) REVERT: D 68 MET cc_start: 0.9324 (mmp) cc_final: 0.8877 (mmp) REVERT: D 90 GLU cc_start: 0.8399 (pt0) cc_final: 0.7392 (pm20) REVERT: E 90 GLU cc_start: 0.8544 (pt0) cc_final: 0.7372 (pm20) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 1.2386 time to fit residues: 202.2703 Evaluate side-chains 145 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 61 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 112 ASN D 112 ASN E 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.098992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.079760 restraints weight = 74339.321| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.49 r_work: 0.2650 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12033 Z= 0.155 Angle : 0.501 7.921 16042 Z= 0.283 Chirality : 0.039 0.136 1705 Planarity : 0.003 0.027 1897 Dihedral : 10.654 59.279 2181 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.77 % Allowed : 9.04 % Favored : 89.18 % 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: 3.31 (0.22), residues: 1384 helix: 2.66 (0.15), residues: 1068 sheet: -2.64 (1.32), residues: 10 loop : 0.71 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS A 180 PHE 0.016 0.002 PHE B 27 TYR 0.024 0.002 TYR C 36 ARG 0.002 0.000 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.06491 ( 841) hydrogen bonds : angle 3.84205 ( 2526) covalent geometry : bond 0.00318 (12028) covalent geometry : angle 0.50062 (16042) Misc. bond : bond 0.00080 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.9023 (tpp) cc_final: 0.8820 (tpp) REVERT: B 74 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8778 (tm) REVERT: B 90 GLU cc_start: 0.8481 (pt0) cc_final: 0.7314 (pm20) REVERT: C 22 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: C 241 MET cc_start: 0.9135 (mtp) cc_final: 0.8832 (mtm) REVERT: D 68 MET cc_start: 0.9323 (mmp) cc_final: 0.8859 (mmp) REVERT: D 90 GLU cc_start: 0.8409 (pt0) cc_final: 0.7409 (pm20) REVERT: E 90 GLU cc_start: 0.8526 (pt0) cc_final: 0.7378 (pm20) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 1.4192 time to fit residues: 227.3255 Evaluate side-chains 145 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 112 ASN D 112 ASN E 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.080859 restraints weight = 73126.449| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.47 r_work: 0.2662 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12033 Z= 0.146 Angle : 0.488 7.507 16042 Z= 0.276 Chirality : 0.039 0.134 1705 Planarity : 0.003 0.027 1897 Dihedral : 10.616 59.886 2181 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.95 % Allowed : 9.04 % Favored : 89.01 % 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: 3.36 (0.21), residues: 1384 helix: 2.66 (0.15), residues: 1069 sheet: None (None), residues: 0 loop : 0.72 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS B 180 PHE 0.015 0.002 PHE B 27 TYR 0.024 0.002 TYR C 36 ARG 0.002 0.000 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.06290 ( 841) hydrogen bonds : angle 3.82247 ( 2526) covalent geometry : bond 0.00295 (12028) covalent geometry : angle 0.48779 (16042) Misc. bond : bond 0.00061 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.935 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.9018 (tpp) cc_final: 0.8802 (tpp) REVERT: B 90 GLU cc_start: 0.8453 (pt0) cc_final: 0.7301 (pm20) REVERT: C 22 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: D 90 GLU cc_start: 0.8402 (pt0) cc_final: 0.7408 (pm20) REVERT: E 90 GLU cc_start: 0.8490 (pt0) cc_final: 0.7381 (pm20) outliers start: 21 outliers final: 12 residues processed: 151 average time/residue: 1.6443 time to fit residues: 270.5139 Evaluate side-chains 145 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 112 ASN D 112 ASN E 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.081400 restraints weight = 88332.791| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.90 r_work: 0.2660 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12033 Z= 0.138 Angle : 0.478 8.058 16042 Z= 0.270 Chirality : 0.038 0.132 1705 Planarity : 0.003 0.027 1897 Dihedral : 10.417 59.511 2181 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.51 % Allowed : 9.66 % Favored : 88.83 % 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: 3.41 (0.21), residues: 1384 helix: 2.71 (0.15), residues: 1069 sheet: None (None), residues: 0 loop : 0.69 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.003 0.001 HIS B 180 PHE 0.014 0.002 PHE B 167 TYR 0.024 0.002 TYR C 36 ARG 0.002 0.000 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.06097 ( 841) hydrogen bonds : angle 3.79847 ( 2526) covalent geometry : bond 0.00273 (12028) covalent geometry : angle 0.47826 (16042) Misc. bond : bond 0.00057 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8964 (tpp) cc_final: 0.8749 (tpp) REVERT: C 22 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: D 90 GLU cc_start: 0.8315 (pt0) cc_final: 0.7379 (pm20) REVERT: E 90 GLU cc_start: 0.8438 (pt0) cc_final: 0.7337 (pm20) outliers start: 16 outliers final: 12 residues processed: 146 average time/residue: 1.3296 time to fit residues: 210.7671 Evaluate side-chains 148 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN E 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.083441 restraints weight = 72156.523| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.71 r_work: 0.2702 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12033 Z= 0.126 Angle : 0.460 7.830 16042 Z= 0.259 Chirality : 0.037 0.128 1705 Planarity : 0.003 0.027 1897 Dihedral : 10.048 59.718 2181 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.33 % Allowed : 9.66 % Favored : 89.01 % 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: 3.49 (0.22), residues: 1384 helix: 2.79 (0.15), residues: 1069 sheet: None (None), residues: 0 loop : 0.64 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 208 HIS 0.003 0.001 HIS B 180 PHE 0.013 0.002 PHE C 167 TYR 0.024 0.001 TYR C 36 ARG 0.002 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.05762 ( 841) hydrogen bonds : angle 3.75584 ( 2526) covalent geometry : bond 0.00238 (12028) covalent geometry : angle 0.46047 (16042) Misc. bond : bond 0.00039 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8982 (tpp) cc_final: 0.8775 (tpp) REVERT: C 22 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: C 241 MET cc_start: 0.9105 (mtp) cc_final: 0.8803 (mtm) REVERT: D 90 GLU cc_start: 0.8408 (pt0) cc_final: 0.7420 (pm20) REVERT: E 90 GLU cc_start: 0.8523 (pt0) cc_final: 0.7402 (pm20) outliers start: 14 outliers final: 11 residues processed: 150 average time/residue: 1.4308 time to fit residues: 232.9097 Evaluate side-chains 151 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN E 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.082400 restraints weight = 80981.139| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.87 r_work: 0.2679 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12033 Z= 0.134 Angle : 0.472 7.842 16042 Z= 0.266 Chirality : 0.038 0.130 1705 Planarity : 0.003 0.027 1897 Dihedral : 10.134 58.915 2181 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.24 % Allowed : 9.93 % Favored : 88.83 % 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: 3.44 (0.21), residues: 1384 helix: 2.74 (0.15), residues: 1069 sheet: None (None), residues: 0 loop : 0.66 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.003 0.001 HIS B 180 PHE 0.014 0.002 PHE C 167 TYR 0.024 0.002 TYR C 36 ARG 0.002 0.000 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.05993 ( 841) hydrogen bonds : angle 3.77699 ( 2526) covalent geometry : bond 0.00258 (12028) covalent geometry : angle 0.47167 (16042) Misc. bond : bond 0.00051 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9698.54 seconds wall clock time: 168 minutes 30.22 seconds (10110.22 seconds total)