Starting phenix.real_space_refine on Thu Sep 18 04:47:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fev_50342/09_2025/9fev_50342.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fev_50342/09_2025/9fev_50342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fev_50342/09_2025/9fev_50342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fev_50342/09_2025/9fev_50342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fev_50342/09_2025/9fev_50342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fev_50342/09_2025/9fev_50342.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 9260 2.51 5 N 2270 2.21 5 O 2615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14225 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2742 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2799 Chain: "B" Number of atoms: 2742 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2799 Chain: "C" Number of atoms: 2742 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2799 Chain: "D" Number of atoms: 2742 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2799 Chain: "E" Number of atoms: 2742 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2799 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N AASN D 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D 41 " occ=0.50 residue: pdb=" N AASN E 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN E 41 " occ=0.50 Time building chain proxies: 6.14, per 1000 atoms: 0.43 Number of scatterers: 14225 At special positions: 0 Unit cell: (100.434, 100.434, 128.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2615 8.00 N 2270 7.00 C 9260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " 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 ALPHA1-3 " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 501 " - " ASN A 8 " " NAG B 501 " - " ASN B 8 " " NAG C 501 " - " ASN C 8 " " NAG D 501 " - " ASN D 8 " " NAG E 501 " - " ASN E 8 " " NAG F 1 " - " ASN A 80 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN C 80 " " NAG I 1 " - " ASN D 80 " " NAG J 1 " - " ASN E 80 " " NAG a 1 " - " ASN A 149 " " NAG b 1 " - " ASN B 149 " " NAG c 1 " - " ASN C 149 " " NAG d 1 " - " ASN D 149 " " NAG e 1 " - " ASN E 149 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 15 sheets defined 44.3% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.822A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.413A pdb=" N ARG A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.588A pdb=" N SER A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.567A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 307 removed outlier: 3.652A pdb=" N PHE A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 446 removed outlier: 3.519A pdb=" N ARG A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.822A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.413A pdb=" N ARG B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 237 removed outlier: 3.588A pdb=" N SER B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.567A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.650A pdb=" N PHE B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 446 removed outlier: 3.520A pdb=" N ARG B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.822A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 4.413A pdb=" N ARG C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.588A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 246 through 272 removed outlier: 3.567A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 307 removed outlier: 3.652A pdb=" N PHE C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 446 removed outlier: 3.519A pdb=" N ARG C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.822A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 4.412A pdb=" N ARG D 142 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 237 removed outlier: 3.588A pdb=" N SER D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 242 Processing helix chain 'D' and resid 246 through 272 removed outlier: 3.567A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 307 removed outlier: 3.651A pdb=" N PHE D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE D 307 " --> pdb=" O ASN D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 446 removed outlier: 3.519A pdb=" N ARG D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.822A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.413A pdb=" N ARG E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.588A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.567A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 307 removed outlier: 3.652A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE E 307 " --> pdb=" O ASN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 446 removed outlier: 3.519A pdb=" N ARG E 428 " --> pdb=" O ASP E 424 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.539A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.538A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.982A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.539A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.538A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR B 176 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 42 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.983A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.539A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.538A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.982A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.540A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.537A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR D 176 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 42 " --> pdb=" O THR D 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.983A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.539A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.537A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR E 176 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE E 42 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.982A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2400 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: 2.82 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4300 1.34 - 1.46: 3452 1.46 - 1.58: 6708 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14600 Sorted by residual: bond pdb=" C1 MAN d 5 " pdb=" O5 MAN d 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C1 MAN c 5 " pdb=" O5 MAN c 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 MAN e 5 " pdb=" O5 MAN e 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 MAN d 4 " pdb=" O5 MAN d 4 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 MAN a 4 " pdb=" O5 MAN a 4 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 14595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 19226 1.08 - 2.16: 419 2.16 - 3.24: 183 3.24 - 4.33: 36 4.33 - 5.41: 16 Bond angle restraints: 19880 Sorted by residual: angle pdb=" C1 BMA c 3 " pdb=" O5 BMA c 3 " pdb=" C5 BMA c 3 " ideal model delta sigma weight residual 118.82 113.41 5.41 3.00e+00 1.11e-01 3.25e+00 angle pdb=" C1 BMA d 3 " pdb=" O5 BMA d 3 " pdb=" C5 BMA d 3 " ideal model delta sigma weight residual 118.82 113.42 5.40 3.00e+00 1.11e-01 3.24e+00 angle pdb=" C1 BMA e 3 " pdb=" O5 BMA e 3 " pdb=" C5 BMA e 3 " ideal model delta sigma weight residual 118.82 113.43 5.39 3.00e+00 1.11e-01 3.23e+00 angle pdb=" C1 BMA b 3 " pdb=" O5 BMA b 3 " pdb=" C5 BMA b 3 " ideal model delta sigma weight residual 118.82 113.44 5.38 3.00e+00 1.11e-01 3.22e+00 angle pdb=" C1 BMA a 3 " pdb=" O5 BMA a 3 " pdb=" C5 BMA a 3 " ideal model delta sigma weight residual 118.82 113.45 5.37 3.00e+00 1.11e-01 3.20e+00 ... (remaining 19875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 8845 21.10 - 42.19: 140 42.19 - 63.29: 30 63.29 - 84.38: 30 84.38 - 105.48: 25 Dihedral angle restraints: 9070 sinusoidal: 4105 harmonic: 4965 Sorted by residual: dihedral pdb=" O4 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C5 BMA b 3 " pdb=" O5 BMA b 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.77 105.48 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C5 BMA d 3 " pdb=" O5 BMA d 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.76 105.47 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.75 105.46 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1931 0.049 - 0.098: 287 0.098 - 0.146: 112 0.146 - 0.195: 10 0.195 - 0.244: 10 Chirality restraints: 2350 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C5 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C6 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C5 BMA e 3 " pdb=" C4 BMA e 3 " pdb=" C6 BMA e 3 " pdb=" O5 BMA e 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2347 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 275 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO D 276 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 276 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 276 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 275 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.31e+00 pdb=" N PRO B 276 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 275 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 276 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.016 5.00e-02 4.00e+02 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2737 2.78 - 3.31: 13159 3.31 - 3.84: 23848 3.84 - 4.37: 28624 4.37 - 4.90: 49381 Nonbonded interactions: 117749 Sorted by model distance: nonbonded pdb=" O THR E 263 " pdb=" ND1 HIS E 267 " model vdw 2.246 3.120 nonbonded pdb=" O THR C 263 " pdb=" ND1 HIS C 267 " model vdw 2.246 3.120 nonbonded pdb=" O THR A 263 " pdb=" ND1 HIS A 267 " model vdw 2.246 3.120 nonbonded pdb=" O THR D 263 " pdb=" ND1 HIS D 267 " model vdw 2.247 3.120 nonbonded pdb=" O THR B 263 " pdb=" ND1 HIS B 267 " model vdw 2.247 3.120 ... (remaining 117744 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 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: 0.630 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.003 0.032 14645 Z= 0.146 Angle : 0.497 5.407 20010 Z= 0.224 Chirality : 0.043 0.244 2350 Planarity : 0.003 0.029 2415 Dihedral : 11.443 105.479 5875 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.67 % Allowed : 2.68 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.21), residues: 1675 helix: 1.76 (0.20), residues: 620 sheet: 1.83 (0.27), residues: 400 loop : 0.79 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.009 0.001 TYR A 66 PHE 0.005 0.001 PHE A 293 TRP 0.005 0.001 TRP E 237 HIS 0.002 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00293 (14600) covalent geometry : angle 0.48952 (19880) SS BOND : bond 0.00036 ( 5) SS BOND : angle 0.33982 ( 10) hydrogen bonds : bond 0.24071 ( 745) hydrogen bonds : angle 7.04965 ( 2400) link_ALPHA1-3 : bond 0.00254 ( 5) link_ALPHA1-3 : angle 1.06590 ( 15) link_ALPHA1-6 : bond 0.00207 ( 5) link_ALPHA1-6 : angle 1.00605 ( 15) link_BETA1-4 : bond 0.00394 ( 15) link_BETA1-4 : angle 1.40932 ( 45) link_NAG-ASN : bond 0.00144 ( 15) link_NAG-ASN : angle 1.18228 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 245 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8397 (mtp) cc_final: 0.7996 (mtt) REVERT: C 9 MET cc_start: 0.8343 (mtp) cc_final: 0.7846 (mtt) REVERT: E 9 MET cc_start: 0.8324 (mtp) cc_final: 0.7985 (mtt) outliers start: 10 outliers final: 5 residues processed: 250 average time/residue: 0.1586 time to fit residues: 54.6205 Evaluate side-chains 165 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 36 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B B 41 ASN B C 41 ASN B D 41 ASN B E 41 ASN B Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040379 restraints weight = 147297.999| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 7.19 r_work: 0.2498 rms_B_bonded: 6.70 restraints_weight: 2.0000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14645 Z= 0.145 Angle : 0.629 9.260 20010 Z= 0.328 Chirality : 0.044 0.160 2350 Planarity : 0.004 0.042 2415 Dihedral : 10.475 82.155 2710 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.27 % Allowed : 7.83 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.22), residues: 1675 helix: 1.99 (0.20), residues: 620 sheet: 1.45 (0.26), residues: 410 loop : 1.06 (0.29), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 213 TYR 0.015 0.001 TYR D 299 PHE 0.011 0.001 PHE C 63 TRP 0.008 0.001 TRP B 67 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00302 (14600) covalent geometry : angle 0.62008 (19880) SS BOND : bond 0.00288 ( 5) SS BOND : angle 0.83193 ( 10) hydrogen bonds : bond 0.05400 ( 745) hydrogen bonds : angle 4.84460 ( 2400) link_ALPHA1-3 : bond 0.00825 ( 5) link_ALPHA1-3 : angle 2.20896 ( 15) link_ALPHA1-6 : bond 0.00423 ( 5) link_ALPHA1-6 : angle 1.99577 ( 15) link_BETA1-4 : bond 0.00457 ( 15) link_BETA1-4 : angle 1.43809 ( 45) link_NAG-ASN : bond 0.00341 ( 15) link_NAG-ASN : angle 0.89716 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.9471 (mmtm) cc_final: 0.9024 (mmpt) REVERT: B 9 MET cc_start: 0.8070 (mtp) cc_final: 0.7517 (mtt) REVERT: B 55 MET cc_start: 0.9384 (mmm) cc_final: 0.8839 (mmm) REVERT: C 9 MET cc_start: 0.7943 (mtp) cc_final: 0.7653 (mtt) REVERT: C 55 MET cc_start: 0.9516 (mmm) cc_final: 0.8900 (mmm) REVERT: C 61 MET cc_start: 0.9681 (OUTLIER) cc_final: 0.9422 (ptp) REVERT: C 115 MET cc_start: 0.9124 (ttm) cc_final: 0.8915 (ttt) REVERT: C 173 LYS cc_start: 0.9714 (mttt) cc_final: 0.9513 (mmmm) REVERT: C 182 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8382 (mm-30) REVERT: C 269 ARG cc_start: 0.8404 (tpt90) cc_final: 0.8126 (tpt90) REVERT: C 274 LYS cc_start: 0.9519 (mmtm) cc_final: 0.9073 (mmpt) REVERT: D 55 MET cc_start: 0.9524 (mmm) cc_final: 0.9075 (mmm) REVERT: D 87 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9007 (p) REVERT: D 90 GLN cc_start: 0.9269 (mt0) cc_final: 0.8973 (mp10) REVERT: D 155 GLU cc_start: 0.9148 (tt0) cc_final: 0.8886 (tt0) REVERT: D 190 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7705 (tm-30) REVERT: E 9 MET cc_start: 0.8136 (mtp) cc_final: 0.7475 (mtt) REVERT: E 55 MET cc_start: 0.9418 (mmm) cc_final: 0.9042 (mmm) REVERT: E 153 GLU cc_start: 0.9095 (mp0) cc_final: 0.8869 (mp0) REVERT: E 244 TYR cc_start: 0.8834 (p90) cc_final: 0.8613 (p90) outliers start: 19 outliers final: 10 residues processed: 205 average time/residue: 0.1604 time to fit residues: 45.3853 Evaluate side-chains 147 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 81 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.055032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.039760 restraints weight = 120594.487| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 6.63 r_work: 0.2505 rms_B_bonded: 6.28 restraints_weight: 2.0000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14645 Z= 0.139 Angle : 0.590 8.084 20010 Z= 0.305 Chirality : 0.044 0.200 2350 Planarity : 0.004 0.029 2415 Dihedral : 9.617 74.516 2710 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.20 % Allowed : 7.69 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.21), residues: 1675 helix: 1.92 (0.20), residues: 620 sheet: 1.48 (0.26), residues: 400 loop : 0.80 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 213 TYR 0.019 0.001 TYR D 299 PHE 0.017 0.001 PHE C 307 TRP 0.009 0.001 TRP B 67 HIS 0.009 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00305 (14600) covalent geometry : angle 0.58096 (19880) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.22456 ( 10) hydrogen bonds : bond 0.04198 ( 745) hydrogen bonds : angle 4.38695 ( 2400) link_ALPHA1-3 : bond 0.00976 ( 5) link_ALPHA1-3 : angle 1.91517 ( 15) link_ALPHA1-6 : bond 0.00697 ( 5) link_ALPHA1-6 : angle 1.99657 ( 15) link_BETA1-4 : bond 0.00299 ( 15) link_BETA1-4 : angle 1.36429 ( 45) link_NAG-ASN : bond 0.00192 ( 15) link_NAG-ASN : angle 1.17355 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.9278 (mtpp) cc_final: 0.9068 (ttmm) REVERT: A 227 MET cc_start: 0.9308 (ttp) cc_final: 0.8615 (tmm) REVERT: B 9 MET cc_start: 0.8125 (mtp) cc_final: 0.7515 (mtt) REVERT: B 55 MET cc_start: 0.9452 (mmm) cc_final: 0.9008 (mmm) REVERT: B 227 MET cc_start: 0.8840 (tmm) cc_final: 0.8592 (tmm) REVERT: B 283 MET cc_start: 0.9584 (tpp) cc_final: 0.9170 (mmt) REVERT: B 286 MET cc_start: 0.9250 (mmp) cc_final: 0.9019 (ppp) REVERT: C 9 MET cc_start: 0.8071 (mtp) cc_final: 0.7796 (mtt) REVERT: C 55 MET cc_start: 0.9506 (mmm) cc_final: 0.8863 (mmm) REVERT: C 61 MET cc_start: 0.9707 (OUTLIER) cc_final: 0.9408 (ptp) REVERT: C 115 MET cc_start: 0.9197 (ttm) cc_final: 0.8996 (ttt) REVERT: C 286 MET cc_start: 0.9203 (mmp) cc_final: 0.8994 (mmp) REVERT: D 9 MET cc_start: 0.8636 (mtt) cc_final: 0.8146 (mtt) REVERT: D 55 MET cc_start: 0.9532 (mmm) cc_final: 0.8902 (mmm) REVERT: D 117 ARG cc_start: 0.9318 (ttm170) cc_final: 0.9113 (tpp80) REVERT: D 137 MET cc_start: 0.9431 (mmm) cc_final: 0.9109 (mmm) REVERT: D 227 MET cc_start: 0.8742 (tmm) cc_final: 0.7947 (tmm) REVERT: E 9 MET cc_start: 0.8277 (mtp) cc_final: 0.7702 (mtt) REVERT: E 55 MET cc_start: 0.9436 (mmm) cc_final: 0.9205 (mmm) REVERT: E 269 ARG cc_start: 0.8321 (tpt170) cc_final: 0.8106 (tpt90) outliers start: 18 outliers final: 15 residues processed: 157 average time/residue: 0.1710 time to fit residues: 36.8538 Evaluate side-chains 143 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 79 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 68 optimal weight: 0.0970 chunk 45 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.039836 restraints weight = 125028.158| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 6.74 r_work: 0.2505 rms_B_bonded: 6.37 restraints_weight: 2.0000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2487 r_free = 0.2487 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14645 Z= 0.123 Angle : 0.571 9.196 20010 Z= 0.288 Chirality : 0.044 0.224 2350 Planarity : 0.003 0.033 2415 Dihedral : 8.795 67.100 2710 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.94 % Allowed : 8.43 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.21), residues: 1675 helix: 1.96 (0.20), residues: 620 sheet: 1.48 (0.26), residues: 400 loop : 0.75 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 269 TYR 0.019 0.002 TYR A 299 PHE 0.012 0.001 PHE D 307 TRP 0.008 0.001 TRP B 67 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00270 (14600) covalent geometry : angle 0.56205 (19880) SS BOND : bond 0.00170 ( 5) SS BOND : angle 0.23389 ( 10) hydrogen bonds : bond 0.03656 ( 745) hydrogen bonds : angle 4.13684 ( 2400) link_ALPHA1-3 : bond 0.00992 ( 5) link_ALPHA1-3 : angle 1.95658 ( 15) link_ALPHA1-6 : bond 0.00862 ( 5) link_ALPHA1-6 : angle 2.08230 ( 15) link_BETA1-4 : bond 0.00324 ( 15) link_BETA1-4 : angle 1.25911 ( 45) link_NAG-ASN : bond 0.00177 ( 15) link_NAG-ASN : angle 1.14170 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.9278 (mtpp) cc_final: 0.9075 (ttmm) REVERT: A 227 MET cc_start: 0.9324 (ttp) cc_final: 0.8330 (tmm) REVERT: B 9 MET cc_start: 0.8121 (mtp) cc_final: 0.7537 (mtt) REVERT: B 55 MET cc_start: 0.9433 (mmm) cc_final: 0.9067 (mmm) REVERT: B 227 MET cc_start: 0.8889 (tmm) cc_final: 0.8297 (tmm) REVERT: B 286 MET cc_start: 0.9232 (mmp) cc_final: 0.8933 (ppp) REVERT: C 9 MET cc_start: 0.8050 (mtp) cc_final: 0.7741 (mtt) REVERT: C 55 MET cc_start: 0.9462 (mmm) cc_final: 0.8876 (mmm) REVERT: C 61 MET cc_start: 0.9693 (OUTLIER) cc_final: 0.9344 (ptp) REVERT: C 112 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8863 (ttpp) REVERT: C 297 LEU cc_start: 0.9741 (mt) cc_final: 0.9416 (mm) REVERT: D 9 MET cc_start: 0.8559 (mtt) cc_final: 0.8344 (mtt) REVERT: D 55 MET cc_start: 0.9519 (mmm) cc_final: 0.8905 (mmm) REVERT: D 137 MET cc_start: 0.9400 (mmm) cc_final: 0.9115 (mmm) REVERT: D 227 MET cc_start: 0.8857 (tmm) cc_final: 0.8129 (tmm) REVERT: D 269 ARG cc_start: 0.8625 (tpt90) cc_final: 0.8422 (tpt90) REVERT: D 274 LYS cc_start: 0.9359 (mmmt) cc_final: 0.8994 (mmmt) REVERT: E 9 MET cc_start: 0.8228 (mtp) cc_final: 0.7836 (mtt) outliers start: 14 outliers final: 13 residues processed: 151 average time/residue: 0.1734 time to fit residues: 35.6964 Evaluate side-chains 147 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.054109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.038917 restraints weight = 144599.722| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 7.09 r_work: 0.2451 rms_B_bonded: 6.58 restraints_weight: 2.0000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14645 Z= 0.153 Angle : 0.571 9.778 20010 Z= 0.286 Chirality : 0.044 0.235 2350 Planarity : 0.003 0.051 2415 Dihedral : 8.384 62.577 2710 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.14 % Allowed : 8.76 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.21), residues: 1675 helix: 2.06 (0.20), residues: 620 sheet: 1.43 (0.25), residues: 400 loop : 0.77 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 269 TYR 0.020 0.001 TYR D 299 PHE 0.009 0.001 PHE E 63 TRP 0.007 0.001 TRP B 67 HIS 0.006 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00336 (14600) covalent geometry : angle 0.56061 (19880) SS BOND : bond 0.00136 ( 5) SS BOND : angle 0.23623 ( 10) hydrogen bonds : bond 0.03523 ( 745) hydrogen bonds : angle 4.08114 ( 2400) link_ALPHA1-3 : bond 0.00947 ( 5) link_ALPHA1-3 : angle 2.13947 ( 15) link_ALPHA1-6 : bond 0.00887 ( 5) link_ALPHA1-6 : angle 2.17240 ( 15) link_BETA1-4 : bond 0.00309 ( 15) link_BETA1-4 : angle 1.28780 ( 45) link_NAG-ASN : bond 0.00098 ( 15) link_NAG-ASN : angle 1.25642 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8102 (mtp) cc_final: 0.7494 (mtt) REVERT: B 55 MET cc_start: 0.9427 (mmm) cc_final: 0.9003 (mmm) REVERT: B 117 ARG cc_start: 0.9297 (ttm170) cc_final: 0.9029 (tpp80) REVERT: B 283 MET cc_start: 0.9586 (tpp) cc_final: 0.9172 (mmt) REVERT: B 286 MET cc_start: 0.9253 (mmp) cc_final: 0.8877 (ppp) REVERT: B 297 LEU cc_start: 0.9725 (mt) cc_final: 0.9372 (mm) REVERT: C 9 MET cc_start: 0.8066 (mtp) cc_final: 0.7791 (mtt) REVERT: C 55 MET cc_start: 0.9481 (mmm) cc_final: 0.8871 (mmm) REVERT: C 61 MET cc_start: 0.9710 (OUTLIER) cc_final: 0.9366 (ptp) REVERT: C 286 MET cc_start: 0.9252 (mmp) cc_final: 0.9033 (mmp) REVERT: C 297 LEU cc_start: 0.9736 (mt) cc_final: 0.9403 (mm) REVERT: D 9 MET cc_start: 0.8510 (mtt) cc_final: 0.8296 (mtt) REVERT: D 55 MET cc_start: 0.9499 (mmm) cc_final: 0.9118 (mmm) REVERT: D 274 LYS cc_start: 0.9344 (mmmt) cc_final: 0.8868 (mmpt) REVERT: E 9 MET cc_start: 0.8267 (mtp) cc_final: 0.7862 (mtt) REVERT: E 55 MET cc_start: 0.9464 (mmm) cc_final: 0.9015 (mmm) outliers start: 17 outliers final: 15 residues processed: 154 average time/residue: 0.1732 time to fit residues: 36.3599 Evaluate side-chains 145 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 121 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.038752 restraints weight = 128013.224| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 6.67 r_work: 0.2452 rms_B_bonded: 6.19 restraints_weight: 2.0000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14645 Z= 0.159 Angle : 0.584 9.300 20010 Z= 0.290 Chirality : 0.045 0.243 2350 Planarity : 0.003 0.038 2415 Dihedral : 8.009 58.417 2710 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.40 % Allowed : 8.63 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.21), residues: 1675 helix: 2.11 (0.20), residues: 620 sheet: 1.40 (0.25), residues: 400 loop : 0.74 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 269 TYR 0.019 0.001 TYR D 299 PHE 0.009 0.001 PHE E 63 TRP 0.006 0.000 TRP B 67 HIS 0.006 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00351 (14600) covalent geometry : angle 0.57343 (19880) SS BOND : bond 0.00128 ( 5) SS BOND : angle 0.21178 ( 10) hydrogen bonds : bond 0.03405 ( 745) hydrogen bonds : angle 4.01935 ( 2400) link_ALPHA1-3 : bond 0.00914 ( 5) link_ALPHA1-3 : angle 2.11860 ( 15) link_ALPHA1-6 : bond 0.00945 ( 5) link_ALPHA1-6 : angle 2.20081 ( 15) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 1.26541 ( 45) link_NAG-ASN : bond 0.00094 ( 15) link_NAG-ASN : angle 1.26480 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9370 (ttp) cc_final: 0.8538 (tmm) REVERT: B 9 MET cc_start: 0.8171 (mtp) cc_final: 0.7526 (mtt) REVERT: B 55 MET cc_start: 0.9425 (mmm) cc_final: 0.8911 (mmm) REVERT: B 297 LEU cc_start: 0.9726 (mt) cc_final: 0.9349 (mm) REVERT: C 9 MET cc_start: 0.8129 (mtp) cc_final: 0.7825 (mtt) REVERT: C 55 MET cc_start: 0.9480 (mmm) cc_final: 0.9032 (mmm) REVERT: C 61 MET cc_start: 0.9718 (OUTLIER) cc_final: 0.9360 (ptp) REVERT: C 286 MET cc_start: 0.9268 (mmp) cc_final: 0.9053 (mmp) REVERT: C 297 LEU cc_start: 0.9727 (mt) cc_final: 0.9399 (mm) REVERT: D 9 MET cc_start: 0.8574 (mtt) cc_final: 0.8349 (mtt) REVERT: D 18 LYS cc_start: 0.9787 (tttt) cc_final: 0.9577 (ptpp) REVERT: D 55 MET cc_start: 0.9443 (mmm) cc_final: 0.9146 (mmm) REVERT: D 297 LEU cc_start: 0.9718 (mt) cc_final: 0.9461 (mm) REVERT: E 9 MET cc_start: 0.8318 (mtp) cc_final: 0.7911 (mtt) REVERT: E 18 LYS cc_start: 0.9786 (tttt) cc_final: 0.9562 (ptpp) REVERT: E 55 MET cc_start: 0.9450 (mmm) cc_final: 0.8842 (mmm) outliers start: 21 outliers final: 17 residues processed: 152 average time/residue: 0.1593 time to fit residues: 33.6330 Evaluate side-chains 147 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.053954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.039252 restraints weight = 117537.265| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 6.43 r_work: 0.2474 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2478 r_free = 0.2478 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14645 Z= 0.126 Angle : 0.579 8.506 20010 Z= 0.286 Chirality : 0.044 0.249 2350 Planarity : 0.003 0.035 2415 Dihedral : 7.631 54.990 2710 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.34 % Allowed : 8.83 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.21), residues: 1675 helix: 2.06 (0.20), residues: 620 sheet: 1.45 (0.25), residues: 400 loop : 0.72 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 269 TYR 0.018 0.001 TYR D 299 PHE 0.011 0.001 PHE E 293 TRP 0.006 0.001 TRP C 67 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00281 (14600) covalent geometry : angle 0.56945 (19880) SS BOND : bond 0.00100 ( 5) SS BOND : angle 0.22099 ( 10) hydrogen bonds : bond 0.03332 ( 745) hydrogen bonds : angle 3.94191 ( 2400) link_ALPHA1-3 : bond 0.00996 ( 5) link_ALPHA1-3 : angle 2.01041 ( 15) link_ALPHA1-6 : bond 0.01024 ( 5) link_ALPHA1-6 : angle 2.14910 ( 15) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 1.21891 ( 45) link_NAG-ASN : bond 0.00122 ( 15) link_NAG-ASN : angle 1.23514 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9321 (ttp) cc_final: 0.8483 (tmm) REVERT: B 9 MET cc_start: 0.8181 (mtp) cc_final: 0.7560 (mtt) REVERT: B 55 MET cc_start: 0.9448 (mmm) cc_final: 0.8909 (mmm) REVERT: B 297 LEU cc_start: 0.9712 (mt) cc_final: 0.9335 (mm) REVERT: C 9 MET cc_start: 0.8150 (mtp) cc_final: 0.7549 (mtt) REVERT: C 55 MET cc_start: 0.9499 (mmm) cc_final: 0.9065 (mmm) REVERT: C 61 MET cc_start: 0.9707 (OUTLIER) cc_final: 0.9329 (ptp) REVERT: C 286 MET cc_start: 0.9245 (mmp) cc_final: 0.9001 (mmp) REVERT: C 297 LEU cc_start: 0.9733 (mt) cc_final: 0.9404 (mm) REVERT: D 9 MET cc_start: 0.8615 (mtt) cc_final: 0.8386 (mtt) REVERT: D 55 MET cc_start: 0.9404 (mmm) cc_final: 0.9037 (mmm) REVERT: D 297 LEU cc_start: 0.9714 (mt) cc_final: 0.9481 (mm) REVERT: E 9 MET cc_start: 0.8333 (mtp) cc_final: 0.7936 (mtt) REVERT: E 55 MET cc_start: 0.9379 (mmm) cc_final: 0.9029 (mmm) REVERT: E 269 ARG cc_start: 0.8545 (tpt90) cc_final: 0.8256 (tpm170) outliers start: 20 outliers final: 16 residues processed: 149 average time/residue: 0.1551 time to fit residues: 32.3591 Evaluate side-chains 146 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 0.0770 chunk 104 optimal weight: 6.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.039675 restraints weight = 146051.936| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 7.00 r_work: 0.2475 rms_B_bonded: 6.59 restraints_weight: 2.0000 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14645 Z= 0.108 Angle : 0.579 9.847 20010 Z= 0.285 Chirality : 0.044 0.251 2350 Planarity : 0.003 0.032 2415 Dihedral : 7.088 50.541 2710 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.27 % Allowed : 8.83 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.21), residues: 1675 helix: 2.06 (0.20), residues: 620 sheet: 1.51 (0.25), residues: 400 loop : 0.74 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 269 TYR 0.017 0.001 TYR E 299 PHE 0.016 0.001 PHE E 293 TRP 0.009 0.001 TRP C 67 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00235 (14600) covalent geometry : angle 0.57035 (19880) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.08889 ( 10) hydrogen bonds : bond 0.03201 ( 745) hydrogen bonds : angle 3.83548 ( 2400) link_ALPHA1-3 : bond 0.01071 ( 5) link_ALPHA1-3 : angle 1.84805 ( 15) link_ALPHA1-6 : bond 0.01104 ( 5) link_ALPHA1-6 : angle 2.08894 ( 15) link_BETA1-4 : bond 0.00424 ( 15) link_BETA1-4 : angle 1.15312 ( 45) link_NAG-ASN : bond 0.00176 ( 15) link_NAG-ASN : angle 1.20431 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9387 (ptm) cc_final: 0.8903 (ppp) REVERT: A 227 MET cc_start: 0.9260 (ttp) cc_final: 0.8591 (tmm) REVERT: A 297 LEU cc_start: 0.9758 (mt) cc_final: 0.9505 (mm) REVERT: B 9 MET cc_start: 0.8119 (mtp) cc_final: 0.7452 (mtt) REVERT: B 55 MET cc_start: 0.9451 (mmm) cc_final: 0.8931 (mmm) REVERT: B 244 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8577 (p90) REVERT: B 297 LEU cc_start: 0.9721 (mt) cc_final: 0.9326 (mm) REVERT: C 9 MET cc_start: 0.8080 (mtp) cc_final: 0.7479 (mtt) REVERT: C 55 MET cc_start: 0.9500 (mmm) cc_final: 0.8927 (mmm) REVERT: C 61 MET cc_start: 0.9681 (OUTLIER) cc_final: 0.9368 (ptp) REVERT: C 286 MET cc_start: 0.9222 (mmp) cc_final: 0.8969 (mmp) REVERT: C 297 LEU cc_start: 0.9735 (mt) cc_final: 0.9420 (mm) REVERT: D 9 MET cc_start: 0.8923 (mtt) cc_final: 0.8398 (mtt) REVERT: D 55 MET cc_start: 0.9436 (mmm) cc_final: 0.9209 (mmm) REVERT: D 297 LEU cc_start: 0.9718 (mt) cc_final: 0.9484 (mm) REVERT: E 9 MET cc_start: 0.8298 (mtp) cc_final: 0.7885 (mtt) REVERT: E 269 ARG cc_start: 0.8593 (tpt90) cc_final: 0.8347 (tpm170) outliers start: 19 outliers final: 16 residues processed: 158 average time/residue: 0.1532 time to fit residues: 33.8488 Evaluate side-chains 153 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 64 optimal weight: 0.0670 chunk 127 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.054384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.039396 restraints weight = 155249.914| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 7.15 r_work: 0.2462 rms_B_bonded: 6.56 restraints_weight: 2.0000 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14645 Z= 0.128 Angle : 0.593 10.004 20010 Z= 0.291 Chirality : 0.045 0.262 2350 Planarity : 0.003 0.044 2415 Dihedral : 6.892 47.815 2710 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.14 % Allowed : 9.30 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.21), residues: 1675 helix: 2.12 (0.20), residues: 620 sheet: 1.52 (0.25), residues: 400 loop : 0.73 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 269 TYR 0.018 0.001 TYR B 299 PHE 0.017 0.001 PHE E 293 TRP 0.007 0.001 TRP C 67 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00289 (14600) covalent geometry : angle 0.58336 (19880) SS BOND : bond 0.00099 ( 5) SS BOND : angle 0.11801 ( 10) hydrogen bonds : bond 0.03163 ( 745) hydrogen bonds : angle 3.82876 ( 2400) link_ALPHA1-3 : bond 0.00930 ( 5) link_ALPHA1-3 : angle 1.97724 ( 15) link_ALPHA1-6 : bond 0.01060 ( 5) link_ALPHA1-6 : angle 2.12603 ( 15) link_BETA1-4 : bond 0.00387 ( 15) link_BETA1-4 : angle 1.21312 ( 45) link_NAG-ASN : bond 0.00100 ( 15) link_NAG-ASN : angle 1.28291 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9407 (ptm) cc_final: 0.8916 (ppp) REVERT: A 227 MET cc_start: 0.9303 (ttp) cc_final: 0.8646 (tmm) REVERT: A 283 MET cc_start: 0.9463 (mmt) cc_final: 0.9154 (tpp) REVERT: A 297 LEU cc_start: 0.9771 (mt) cc_final: 0.9518 (mm) REVERT: B 9 MET cc_start: 0.8203 (mtp) cc_final: 0.7583 (mtt) REVERT: B 55 MET cc_start: 0.9453 (mmm) cc_final: 0.8934 (mmm) REVERT: B 297 LEU cc_start: 0.9738 (mt) cc_final: 0.9351 (mm) REVERT: C 9 MET cc_start: 0.8131 (mtp) cc_final: 0.7548 (mtt) REVERT: C 55 MET cc_start: 0.9508 (mmm) cc_final: 0.9083 (mmm) REVERT: C 61 MET cc_start: 0.9706 (OUTLIER) cc_final: 0.9372 (ptp) REVERT: C 286 MET cc_start: 0.9276 (mmp) cc_final: 0.9026 (mmp) REVERT: C 297 LEU cc_start: 0.9741 (mt) cc_final: 0.9426 (mm) REVERT: D 9 MET cc_start: 0.8955 (mtt) cc_final: 0.8441 (mtt) REVERT: D 55 MET cc_start: 0.9413 (mmm) cc_final: 0.9094 (mmm) REVERT: D 297 LEU cc_start: 0.9726 (mt) cc_final: 0.9493 (mm) REVERT: E 9 MET cc_start: 0.8326 (mtp) cc_final: 0.7962 (mtt) REVERT: E 55 MET cc_start: 0.9483 (mmm) cc_final: 0.8929 (mmm) REVERT: E 227 MET cc_start: 0.9032 (tmm) cc_final: 0.8701 (tmm) REVERT: E 269 ARG cc_start: 0.8610 (tpt90) cc_final: 0.8353 (tpm170) outliers start: 17 outliers final: 16 residues processed: 148 average time/residue: 0.1570 time to fit residues: 32.5470 Evaluate side-chains 154 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 143 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.0170 chunk 19 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 overall best weight: 1.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.039210 restraints weight = 129655.977| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 6.69 r_work: 0.2470 rms_B_bonded: 6.36 restraints_weight: 2.0000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14645 Z= 0.136 Angle : 0.593 9.909 20010 Z= 0.292 Chirality : 0.045 0.247 2350 Planarity : 0.003 0.043 2415 Dihedral : 6.594 42.495 2710 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.14 % Allowed : 9.50 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.21), residues: 1675 helix: 2.16 (0.20), residues: 620 sheet: 1.55 (0.25), residues: 400 loop : 0.71 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 269 TYR 0.017 0.001 TYR B 299 PHE 0.016 0.001 PHE E 293 TRP 0.006 0.000 TRP B 67 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00306 (14600) covalent geometry : angle 0.58374 (19880) SS BOND : bond 0.00093 ( 5) SS BOND : angle 0.15848 ( 10) hydrogen bonds : bond 0.03158 ( 745) hydrogen bonds : angle 3.82397 ( 2400) link_ALPHA1-3 : bond 0.00927 ( 5) link_ALPHA1-3 : angle 1.89414 ( 15) link_ALPHA1-6 : bond 0.01058 ( 5) link_ALPHA1-6 : angle 2.01856 ( 15) link_BETA1-4 : bond 0.00424 ( 15) link_BETA1-4 : angle 1.22930 ( 45) link_NAG-ASN : bond 0.00090 ( 15) link_NAG-ASN : angle 1.28843 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9803 (tttt) cc_final: 0.9583 (ptpp) REVERT: A 49 MET cc_start: 0.9373 (ptm) cc_final: 0.8855 (ppp) REVERT: A 227 MET cc_start: 0.9311 (ttp) cc_final: 0.8657 (tmm) REVERT: A 283 MET cc_start: 0.9451 (mmt) cc_final: 0.9186 (tpp) REVERT: A 297 LEU cc_start: 0.9774 (mt) cc_final: 0.9523 (mm) REVERT: B 9 MET cc_start: 0.8196 (mtp) cc_final: 0.7567 (mtt) REVERT: B 55 MET cc_start: 0.9454 (mmm) cc_final: 0.8899 (mmm) REVERT: B 297 LEU cc_start: 0.9744 (mt) cc_final: 0.9369 (mm) REVERT: C 9 MET cc_start: 0.8128 (mtp) cc_final: 0.7545 (mtt) REVERT: C 55 MET cc_start: 0.9511 (mmm) cc_final: 0.9098 (mmm) REVERT: C 61 MET cc_start: 0.9719 (OUTLIER) cc_final: 0.9390 (ptp) REVERT: C 286 MET cc_start: 0.9305 (mmp) cc_final: 0.9087 (mmp) REVERT: C 297 LEU cc_start: 0.9740 (mt) cc_final: 0.9423 (mm) REVERT: D 9 MET cc_start: 0.8625 (mtt) cc_final: 0.8381 (mtt) REVERT: D 55 MET cc_start: 0.9399 (mmm) cc_final: 0.9079 (mmm) REVERT: D 297 LEU cc_start: 0.9720 (mt) cc_final: 0.9492 (mm) REVERT: E 9 MET cc_start: 0.8326 (mtp) cc_final: 0.7989 (mtt) REVERT: E 227 MET cc_start: 0.9051 (tmm) cc_final: 0.8710 (tmm) REVERT: E 269 ARG cc_start: 0.8628 (tpt90) cc_final: 0.8348 (tpm170) outliers start: 17 outliers final: 16 residues processed: 150 average time/residue: 0.1514 time to fit residues: 31.4975 Evaluate side-chains 153 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 107 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 50 optimal weight: 0.0030 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.040079 restraints weight = 109158.707| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 6.23 r_work: 0.2507 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14645 Z= 0.109 Angle : 0.590 10.929 20010 Z= 0.290 Chirality : 0.044 0.229 2350 Planarity : 0.003 0.042 2415 Dihedral : 6.266 51.703 2710 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.07 % Allowed : 9.50 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.21), residues: 1675 helix: 2.10 (0.20), residues: 620 sheet: 1.57 (0.25), residues: 400 loop : 0.69 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 269 TYR 0.017 0.001 TYR B 299 PHE 0.017 0.001 PHE E 293 TRP 0.008 0.001 TRP C 67 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00245 (14600) covalent geometry : angle 0.58200 (19880) SS BOND : bond 0.00099 ( 5) SS BOND : angle 0.10664 ( 10) hydrogen bonds : bond 0.03096 ( 745) hydrogen bonds : angle 3.73832 ( 2400) link_ALPHA1-3 : bond 0.00987 ( 5) link_ALPHA1-3 : angle 1.66971 ( 15) link_ALPHA1-6 : bond 0.01066 ( 5) link_ALPHA1-6 : angle 1.79799 ( 15) link_BETA1-4 : bond 0.00494 ( 15) link_BETA1-4 : angle 1.20559 ( 45) link_NAG-ASN : bond 0.00175 ( 15) link_NAG-ASN : angle 1.22029 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3766.31 seconds wall clock time: 65 minutes 29.78 seconds (3929.78 seconds total)