Starting phenix.real_space_refine on Thu Mar 13 02:02:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c48_45177/03_2025/9c48_45177.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c48_45177/03_2025/9c48_45177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c48_45177/03_2025/9c48_45177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c48_45177/03_2025/9c48_45177.map" model { file = "/net/cci-nas-00/data/ceres_data/9c48_45177/03_2025/9c48_45177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c48_45177/03_2025/9c48_45177.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 5202 2.51 5 N 1341 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8481 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 2613 Chain: "B" Number of atoms: 2575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 2613 Chain: "C" Number of atoms: 2575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 2613 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN A 94 " occ=0.62 ... (16 atoms not shown) pdb=" NE2BGLN A 94 " occ=0.38 residue: pdb=" N AGLN B 94 " occ=0.62 ... (16 atoms not shown) pdb=" NE2BGLN B 94 " occ=0.38 residue: pdb=" N AGLN C 94 " occ=0.62 ... (16 atoms not shown) pdb=" NE2BGLN C 94 " occ=0.38 Time building chain proxies: 12.66, per 1000 atoms: 1.49 Number of scatterers: 8481 At special positions: 0 Unit cell: (87.48, 86.184, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 9 15.00 Mg 3 11.99 O 1866 8.00 N 1341 7.00 C 5202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 402 " - " ASN A 75 " " NAG A 403 " - " ASN A 110 " " NAG A 404 " - " ASN A 153 " " NAG B 503 " - " ASN B 75 " " NAG B 504 " - " ASN B 110 " " NAG B 505 " - " ASN B 153 " " NAG C 503 " - " ASN C 75 " " NAG C 504 " - " ASN C 110 " " NAG C 505 " - " ASN C 153 " " NAG D 1 " - " ASN A 184 " " NAG E 1 " - " ASN A 199 " " NAG F 1 " - " ASN A 208 " " NAG G 1 " - " ASN B 184 " " NAG H 1 " - " ASN B 199 " " NAG I 1 " - " ASN B 208 " " NAG J 1 " - " ASN C 184 " " NAG K 1 " - " ASN C 199 " " NAG L 1 " - " ASN C 208 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1854 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 15 sheets defined 25.8% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.926A pdb=" N SER A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.865A pdb=" N VAL A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 331 through 361 removed outlier: 3.679A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.927A pdb=" N SER B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.865A pdb=" N VAL B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 331 through 361 removed outlier: 3.679A pdb=" N THR B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.926A pdb=" N SER C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.865A pdb=" N VAL C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 331 through 361 removed outlier: 3.680A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 3.682A pdb=" N CYS A 261 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.350A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69 removed outlier: 3.757A pdb=" N PHE A 200 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA5, first strand: chain 'A' and resid 72 through 76 Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 59 removed outlier: 3.681A pdb=" N CYS B 261 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.350A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 69 removed outlier: 3.757A pdb=" N PHE B 200 " --> pdb=" O TYR B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 76 Processing sheet with id=AB2, first strand: chain 'C' and resid 55 through 59 removed outlier: 3.681A pdb=" N CYS C 261 " --> pdb=" O LYS C 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.350A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 61 through 69 removed outlier: 3.758A pdb=" N PHE C 200 " --> pdb=" O TYR C 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 76 379 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2551 1.34 - 1.46: 1989 1.46 - 1.58: 3773 1.58 - 1.70: 12 1.70 - 1.82: 84 Bond restraints: 8409 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 1.374 1.329 0.045 1.00e-02 1.00e+04 2.06e+01 bond pdb=" C4 ATP B 502 " pdb=" N9 ATP B 502 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" C4 ATP C 502 " pdb=" N9 ATP C 502 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.94e+01 bond pdb=" C8 ATP C 502 " pdb=" N7 ATP C 502 " ideal model delta sigma weight residual 1.310 1.353 -0.043 1.00e-02 1.00e+04 1.87e+01 bond pdb=" C3' ATP A 401 " pdb=" C4' ATP A 401 " ideal model delta sigma weight residual 1.526 1.573 -0.047 1.10e-02 8.26e+03 1.83e+01 ... (remaining 8404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 11397 3.75 - 7.49: 63 7.49 - 11.24: 0 11.24 - 14.98: 0 14.98 - 18.73: 6 Bond angle restraints: 11466 Sorted by residual: angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 121.18 18.69 1.00e+00 1.00e+00 3.49e+02 angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 121.19 18.68 1.00e+00 1.00e+00 3.49e+02 angle pdb=" PA ATP B 502 " pdb=" O3A ATP B 502 " pdb=" PB ATP B 502 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP C 502 " pdb=" O3A ATP C 502 " pdb=" PB ATP C 502 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 ... (remaining 11461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 5010 21.20 - 42.41: 309 42.41 - 63.61: 63 63.61 - 84.82: 33 84.82 - 106.02: 12 Dihedral angle restraints: 5427 sinusoidal: 2541 harmonic: 2886 Sorted by residual: dihedral pdb=" CB CYS B 261 " pdb=" SG CYS B 261 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual 93.00 51.69 41.31 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CB CYS C 261 " pdb=" SG CYS C 261 " pdb=" SG CYS C 270 " pdb=" CB CYS C 270 " ideal model delta sinusoidal sigma weight residual 93.00 51.69 41.31 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CB CYS A 261 " pdb=" SG CYS A 261 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual 93.00 51.71 41.29 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 5424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1020 0.054 - 0.108: 256 0.108 - 0.162: 92 0.162 - 0.216: 21 0.216 - 0.269: 6 Chirality restraints: 1395 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1392 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 110 " 0.022 2.00e-02 2.50e+03 2.03e-02 5.16e+00 pdb=" CG ASN B 110 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 110 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 110 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG B 504 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 110 " -0.022 2.00e-02 2.50e+03 2.01e-02 5.07e+00 pdb=" CG ASN A 110 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 110 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 110 " 0.020 2.00e-02 2.50e+03 pdb=" C1 NAG A 403 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 110 " 0.022 2.00e-02 2.50e+03 2.00e-02 5.00e+00 pdb=" CG ASN C 110 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 110 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 110 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG C 504 " 0.022 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1341 2.77 - 3.30: 7791 3.30 - 3.83: 14313 3.83 - 4.37: 18443 4.37 - 4.90: 29492 Nonbonded interactions: 71380 Sorted by model distance: nonbonded pdb=" OE2 GLU A 95 " pdb=" O HOH A 501 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU C 95 " pdb=" O HOH C 601 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU B 95 " pdb=" O HOH B 601 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASP B 88 " pdb=" OH TYR C 299 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR A 299 " pdb=" OD1 ASP C 88 " model vdw 2.261 3.040 ... (remaining 71375 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 93 or resid 95 through 361 or resid 403 through \ 404)) selection = (chain 'B' and (resid 31 through 93 or resid 95 through 361 or resid 503 through \ 504)) selection = (chain 'C' and (resid 31 through 93 or resid 95 through 361 or resid 503 through \ 504)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 99.660 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 32.020 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8409 Z= 0.381 Angle : 0.901 18.729 11466 Z= 0.632 Chirality : 0.060 0.269 1395 Planarity : 0.004 0.031 1404 Dihedral : 16.098 106.020 3537 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: -0.49 (0.26), residues: 996 helix: -1.00 (0.31), residues: 270 sheet: 0.44 (0.28), residues: 333 loop : -0.30 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 164 HIS 0.001 0.000 HIS A 286 PHE 0.011 0.002 PHE B 198 TYR 0.008 0.001 TYR B 89 ARG 0.005 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.932 Fit side-chains REVERT: B 326 LYS cc_start: 0.8475 (pttt) cc_final: 0.8257 (pptt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 1.6499 time to fit residues: 142.7135 Evaluate side-chains 81 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 308 GLN B 338 ASN C 175 GLN C 308 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.120689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.081530 restraints weight = 29910.215| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.45 r_work: 0.2877 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8409 Z= 0.286 Angle : 0.622 7.111 11466 Z= 0.328 Chirality : 0.050 0.218 1395 Planarity : 0.004 0.032 1404 Dihedral : 12.158 79.639 1800 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.30 % Allowed : 11.74 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: -0.29 (0.25), residues: 996 helix: -0.10 (0.31), residues: 270 sheet: 0.22 (0.26), residues: 369 loop : -0.51 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 164 HIS 0.004 0.001 HIS A 286 PHE 0.011 0.002 PHE A 81 TYR 0.014 0.002 TYR C 89 ARG 0.004 0.001 ARG C 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 95 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 51 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 326 LYS cc_start: 0.8680 (pttt) cc_final: 0.8081 (pptt) REVERT: C 51 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7742 (mm-30) outliers start: 11 outliers final: 5 residues processed: 99 average time/residue: 1.8890 time to fit residues: 196.6163 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 18 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 244 GLN A 287 ASN B 175 GLN B 308 GLN C 175 GLN C 308 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082853 restraints weight = 37664.420| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.02 r_work: 0.2883 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 8409 Z= 0.196 Angle : 0.525 5.394 11466 Z= 0.280 Chirality : 0.047 0.263 1395 Planarity : 0.003 0.031 1404 Dihedral : 9.671 78.916 1800 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.95 % Allowed : 11.63 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.11 (0.26), residues: 996 helix: 0.78 (0.34), residues: 252 sheet: 0.26 (0.26), residues: 366 loop : -0.46 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 259 HIS 0.003 0.001 HIS A 286 PHE 0.008 0.002 PHE C 81 TYR 0.014 0.001 TYR A 89 ARG 0.002 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 95 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 307 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: A 326 LYS cc_start: 0.8556 (pttp) cc_final: 0.7946 (pptt) REVERT: B 51 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7767 (mm-30) REVERT: B 307 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 308 GLN cc_start: 0.8477 (mt0) cc_final: 0.8244 (mt0) REVERT: B 326 LYS cc_start: 0.8695 (pttt) cc_final: 0.8161 (pptt) REVERT: C 51 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 95 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7642 (mt-10) REVERT: C 326 LYS cc_start: 0.8591 (pttp) cc_final: 0.7982 (pptt) outliers start: 8 outliers final: 0 residues processed: 97 average time/residue: 1.6764 time to fit residues: 170.7581 Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 244 GLN A 287 ASN B 175 GLN C 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.120376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.081052 restraints weight = 30576.078| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.44 r_work: 0.2870 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8409 Z= 0.256 Angle : 0.560 5.409 11466 Z= 0.299 Chirality : 0.048 0.245 1395 Planarity : 0.004 0.033 1404 Dihedral : 9.617 76.994 1800 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.95 % Allowed : 12.57 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.09 (0.26), residues: 996 helix: 0.77 (0.34), residues: 252 sheet: 0.29 (0.26), residues: 366 loop : -0.51 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 164 HIS 0.004 0.001 HIS A 286 PHE 0.011 0.002 PHE C 294 TYR 0.012 0.001 TYR C 89 ARG 0.002 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 95 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 326 LYS cc_start: 0.8554 (pttp) cc_final: 0.7912 (pptt) REVERT: B 51 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 307 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7634 (mm-30) REVERT: B 308 GLN cc_start: 0.8527 (mt0) cc_final: 0.8301 (mt0) REVERT: B 326 LYS cc_start: 0.8703 (pttt) cc_final: 0.8166 (pptt) REVERT: C 51 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7734 (mm-30) REVERT: C 95 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7640 (mt-10) REVERT: C 260 ASP cc_start: 0.8382 (t70) cc_final: 0.8155 (t0) REVERT: C 307 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: C 326 LYS cc_start: 0.8570 (pttp) cc_final: 0.7999 (pptt) outliers start: 8 outliers final: 4 residues processed: 97 average time/residue: 1.6576 time to fit residues: 169.4085 Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 307 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 244 GLN A 287 ASN B 175 GLN C 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.081358 restraints weight = 38425.492| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.04 r_work: 0.2869 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8409 Z= 0.265 Angle : 0.564 5.461 11466 Z= 0.300 Chirality : 0.048 0.244 1395 Planarity : 0.004 0.034 1404 Dihedral : 9.639 76.217 1800 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.95 % Allowed : 12.69 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.06 (0.26), residues: 996 helix: 0.76 (0.34), residues: 252 sheet: 0.31 (0.26), residues: 366 loop : -0.60 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 259 HIS 0.004 0.001 HIS A 286 PHE 0.011 0.002 PHE C 294 TYR 0.011 0.001 TYR C 89 ARG 0.002 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7935 (mm-30) REVERT: A 95 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 326 LYS cc_start: 0.8608 (pttp) cc_final: 0.8004 (pptt) REVERT: B 51 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 307 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 308 GLN cc_start: 0.8603 (mt0) cc_final: 0.8262 (mt0) REVERT: B 326 LYS cc_start: 0.8737 (pttt) cc_final: 0.8202 (pptt) REVERT: C 51 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7655 (mm-30) REVERT: C 95 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 260 ASP cc_start: 0.8392 (t70) cc_final: 0.8184 (t0) REVERT: C 307 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: C 308 GLN cc_start: 0.8549 (mt0) cc_final: 0.8335 (mt0) REVERT: C 326 LYS cc_start: 0.8606 (pttp) cc_final: 0.8060 (pptt) outliers start: 8 outliers final: 3 residues processed: 97 average time/residue: 1.9901 time to fit residues: 203.3485 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 307 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 175 GLN C 175 GLN C 244 GLN C 308 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.120993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.082524 restraints weight = 28455.462| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.73 r_work: 0.2901 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8409 Z= 0.192 Angle : 0.519 5.452 11466 Z= 0.277 Chirality : 0.046 0.228 1395 Planarity : 0.003 0.033 1404 Dihedral : 9.347 75.723 1800 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.83 % Allowed : 13.17 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.16 (0.26), residues: 996 helix: 0.95 (0.34), residues: 252 sheet: 0.30 (0.26), residues: 366 loop : -0.55 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 259 HIS 0.003 0.001 HIS A 286 PHE 0.009 0.001 PHE C 294 TYR 0.011 0.001 TYR C 89 ARG 0.001 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 95 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 326 LYS cc_start: 0.8577 (pttp) cc_final: 0.8013 (pptt) REVERT: B 51 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 307 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 308 GLN cc_start: 0.8575 (mt0) cc_final: 0.8241 (mt0) REVERT: B 326 LYS cc_start: 0.8709 (pttt) cc_final: 0.8231 (pptt) REVERT: C 51 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7630 (mm-30) REVERT: C 95 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 307 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: C 326 LYS cc_start: 0.8566 (pttp) cc_final: 0.8052 (pptt) outliers start: 7 outliers final: 3 residues processed: 97 average time/residue: 2.2123 time to fit residues: 225.8152 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 307 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 0.0040 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 175 GLN C 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.121240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.082518 restraints weight = 39293.062| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.05 r_work: 0.2893 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 8409 Z= 0.180 Angle : 0.517 6.684 11466 Z= 0.274 Chirality : 0.046 0.214 1395 Planarity : 0.003 0.033 1404 Dihedral : 9.187 75.683 1800 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.07 % Allowed : 13.52 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.23 (0.26), residues: 996 helix: 1.07 (0.34), residues: 252 sheet: 0.33 (0.26), residues: 366 loop : -0.53 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 259 HIS 0.002 0.001 HIS A 286 PHE 0.009 0.001 PHE C 294 TYR 0.011 0.001 TYR A 89 ARG 0.001 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 95 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 326 LYS cc_start: 0.8558 (pttp) cc_final: 0.8001 (pptt) REVERT: B 51 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 307 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 308 GLN cc_start: 0.8605 (mt0) cc_final: 0.8294 (mt0) REVERT: B 326 LYS cc_start: 0.8684 (pttt) cc_final: 0.8216 (pptt) REVERT: C 51 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7703 (mm-30) REVERT: C 95 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7609 (mt-10) REVERT: C 307 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: C 308 GLN cc_start: 0.8500 (mt0) cc_final: 0.8217 (mt0) REVERT: C 326 LYS cc_start: 0.8586 (pttp) cc_final: 0.8035 (pptt) outliers start: 9 outliers final: 5 residues processed: 95 average time/residue: 1.6995 time to fit residues: 169.6769 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 307 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 287 ASN B 175 GLN C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.120223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081691 restraints weight = 37444.246| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.83 r_work: 0.2879 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8409 Z= 0.248 Angle : 0.555 5.472 11466 Z= 0.295 Chirality : 0.047 0.218 1395 Planarity : 0.004 0.034 1404 Dihedral : 9.445 75.567 1800 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.95 % Allowed : 13.76 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.12 (0.26), residues: 996 helix: 0.94 (0.34), residues: 252 sheet: 0.29 (0.26), residues: 366 loop : -0.60 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 164 HIS 0.003 0.001 HIS B 286 PHE 0.010 0.002 PHE C 294 TYR 0.011 0.001 TYR A 89 ARG 0.002 0.000 ARG C 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 95 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 326 LYS cc_start: 0.8584 (pttp) cc_final: 0.8020 (pptt) REVERT: B 51 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 326 LYS cc_start: 0.8712 (pttt) cc_final: 0.8248 (pptt) REVERT: C 51 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7737 (mm-30) REVERT: C 95 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7643 (mt-10) REVERT: C 307 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7743 (mm-30) REVERT: C 326 LYS cc_start: 0.8598 (pttp) cc_final: 0.8053 (pptt) outliers start: 8 outliers final: 4 residues processed: 99 average time/residue: 1.5720 time to fit residues: 163.8781 Evaluate side-chains 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 0.2980 chunk 26 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 287 ASN B 175 GLN C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.120432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.081442 restraints weight = 41263.781| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.27 r_work: 0.2854 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8409 Z= 0.243 Angle : 0.557 6.217 11466 Z= 0.295 Chirality : 0.047 0.257 1395 Planarity : 0.004 0.034 1404 Dihedral : 9.444 75.475 1800 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.71 % Allowed : 13.64 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.12 (0.26), residues: 996 helix: 0.96 (0.34), residues: 252 sheet: 0.28 (0.26), residues: 366 loop : -0.61 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 259 HIS 0.003 0.001 HIS C 286 PHE 0.010 0.002 PHE C 294 TYR 0.011 0.001 TYR A 89 ARG 0.002 0.000 ARG C 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 95 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 326 LYS cc_start: 0.8596 (pttp) cc_final: 0.8037 (pptt) REVERT: B 51 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 326 LYS cc_start: 0.8726 (pttt) cc_final: 0.8253 (pptt) REVERT: C 51 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7762 (mm-30) REVERT: C 95 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 307 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7791 (mm-30) REVERT: C 326 LYS cc_start: 0.8619 (pttp) cc_final: 0.8068 (pptt) outliers start: 6 outliers final: 4 residues processed: 97 average time/residue: 1.6186 time to fit residues: 165.1944 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.0060 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 308 GLN B 175 GLN C 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.080951 restraints weight = 41807.689| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.32 r_work: 0.2848 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8409 Z= 0.269 Angle : 0.571 5.498 11466 Z= 0.303 Chirality : 0.048 0.212 1395 Planarity : 0.004 0.034 1404 Dihedral : 9.580 75.400 1800 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.83 % Allowed : 13.40 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.07 (0.26), residues: 996 helix: 0.91 (0.34), residues: 252 sheet: 0.26 (0.26), residues: 366 loop : -0.64 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 259 HIS 0.004 0.001 HIS B 286 PHE 0.011 0.002 PHE C 294 TYR 0.010 0.001 TYR A 89 ARG 0.002 0.000 ARG B 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 95 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 326 LYS cc_start: 0.8614 (pttp) cc_final: 0.8058 (pptt) REVERT: B 51 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 326 LYS cc_start: 0.8735 (pttt) cc_final: 0.8260 (pptt) REVERT: C 51 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 95 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7674 (mt-10) REVERT: C 326 LYS cc_start: 0.8631 (pttp) cc_final: 0.8078 (pptt) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 1.7474 time to fit residues: 178.3741 Evaluate side-chains 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.2316 > 50: distance: 18 - 166: 28.841 distance: 21 - 163: 27.692 distance: 33 - 147: 36.710 distance: 36 - 144: 33.663 distance: 45 - 135: 35.241 distance: 48 - 132: 11.450 distance: 50 - 168: 32.633 distance: 101 - 123: 31.671 distance: 119 - 123: 33.085 distance: 123 - 124: 28.888 distance: 124 - 125: 41.476 distance: 124 - 127: 26.589 distance: 125 - 132: 35.744 distance: 127 - 128: 43.207 distance: 128 - 129: 19.638 distance: 129 - 130: 40.248 distance: 129 - 131: 9.587 distance: 132 - 133: 22.333 distance: 133 - 134: 27.176 distance: 133 - 136: 44.380 distance: 134 - 135: 41.549 distance: 134 - 139: 14.226 distance: 136 - 137: 16.109 distance: 136 - 138: 50.856 distance: 140 - 143: 27.412 distance: 141 - 142: 40.280 distance: 144 - 145: 47.818 distance: 145 - 146: 15.335 distance: 145 - 148: 28.571 distance: 146 - 147: 8.431 distance: 146 - 149: 51.687 distance: 149 - 150: 26.707 distance: 150 - 151: 12.382 distance: 150 - 153: 56.521 distance: 151 - 152: 15.777 distance: 151 - 163: 26.181 distance: 153 - 154: 17.967 distance: 154 - 155: 29.784 distance: 154 - 156: 3.678 distance: 155 - 157: 37.221 distance: 156 - 158: 13.738 distance: 156 - 159: 18.445 distance: 157 - 158: 23.417 distance: 158 - 160: 27.125 distance: 159 - 161: 27.636 distance: 160 - 162: 15.317 distance: 161 - 162: 20.543 distance: 163 - 164: 45.551 distance: 164 - 165: 50.558 distance: 164 - 167: 18.725 distance: 165 - 166: 44.939 distance: 165 - 169: 12.728 distance: 167 - 168: 16.826 distance: 169 - 170: 17.556 distance: 169 - 175: 15.044 distance: 170 - 171: 28.048 distance: 170 - 173: 35.937 distance: 171 - 172: 24.205 distance: 171 - 176: 24.703 distance: 173 - 174: 35.794 distance: 174 - 175: 43.638 distance: 176 - 177: 10.126 distance: 177 - 178: 25.099 distance: 177 - 180: 30.275 distance: 178 - 179: 6.270 distance: 178 - 183: 53.227 distance: 180 - 181: 17.367 distance: 180 - 182: 6.510 distance: 183 - 184: 18.887 distance: 184 - 185: 47.789 distance: 184 - 187: 23.278 distance: 185 - 186: 10.790 distance: 185 - 192: 35.033 distance: 188 - 189: 17.372 distance: 189 - 190: 28.387 distance: 189 - 191: 5.211 distance: 192 - 193: 7.346 distance: 193 - 194: 29.118 distance: 193 - 196: 5.934 distance: 194 - 195: 25.863 distance: 194 - 200: 8.259 distance: 196 - 197: 21.846 distance: 197 - 198: 21.977 distance: 197 - 199: 19.957