Starting phenix.real_space_refine on Thu Sep 18 05:09:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9few_50343/09_2025/9few_50343.cif Found real_map, /net/cci-nas-00/data/ceres_data/9few_50343/09_2025/9few_50343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9few_50343/09_2025/9few_50343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9few_50343/09_2025/9few_50343.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9few_50343/09_2025/9few_50343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9few_50343/09_2025/9few_50343.map" } resolution = 3.5 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 9265 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 11 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: 14230 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: 2747 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: 2793 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: 6.29, per 1000 atoms: 0.44 Number of scatterers: 14230 At special positions: 0 Unit cell: (99.1936, 100.434, 127.712, 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 9265 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: 1.64 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 42.9% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 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: 3.733A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (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: 3.784A pdb=" N SER A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.650A 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 Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 446 removed outlier: 3.686A 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: 3.798A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.352A pdb=" N ARG B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 removed outlier: 3.588A pdb=" N LYS B 173 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 246 through 272 Processing helix chain 'B' and resid 279 through 307 removed outlier: 4.344A pdb=" N PHE B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 446 removed outlier: 3.674A 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: 3.591A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (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: 3.702A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.650A 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 Processing helix chain 'C' and resid 279 through 307 removed outlier: 4.506A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 446 removed outlier: 3.591A pdb=" N ARG C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) removed outlier: 4.229A 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 69 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.017A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (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: 3.587A pdb=" N SER D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 3.644A 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: 3.707A pdb=" N ARG D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 305 Processing helix chain 'D' and resid 309 through 446 removed outlier: 3.530A 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 90 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: 3.595A 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 Processing helix chain 'E' and resid 279 through 307 removed outlier: 4.337A pdb=" N PHE E 307 " --> pdb=" O ASN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 446 removed outlier: 3.957A 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: 4.292A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 60 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE A 47 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 45 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN A 64 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP A 43 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N TYR A 66 " --> pdb=" O AASN A 41 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N AASN A 41 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ARG A 68 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLY A 39 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.344A pdb=" N ASP A 101 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 135 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 103 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 60 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE A 47 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 45 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN A 64 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP A 43 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N TYR A 66 " --> pdb=" O AASN A 41 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N AASN A 41 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ARG A 68 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLY A 39 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.819A 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 97 removed outlier: 4.245A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A 205 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN A 197 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG A 207 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A 195 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A 209 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 193 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER A 211 " --> pdb=" O HIS A 191 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG A 213 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.331A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.556A 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: 6.727A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.172A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR B 205 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN B 197 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B 207 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER B 195 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER B 209 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU B 193 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER B 211 " --> pdb=" O HIS B 191 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS B 191 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG B 213 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.130A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR C 60 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE C 47 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N TYR C 62 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA C 45 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLN C 64 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASP C 43 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TYR C 66 " --> pdb=" O AASN C 41 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N AASN C 41 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N ARG C 68 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N GLY C 39 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.761A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR C 60 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE C 47 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N TYR C 62 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA C 45 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLN C 64 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASP C 43 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TYR C 66 " --> pdb=" O AASN C 41 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N AASN C 41 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N ARG C 68 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N GLY C 39 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.836A 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: 4.422A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.627A 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: 4.153A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.815A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 4.069A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR D 205 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN D 197 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG D 207 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER D 195 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER D 209 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU D 193 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER D 211 " --> pdb=" O HIS D 191 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS D 191 " --> pdb=" O SER D 211 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG D 213 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.258A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.629A 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: 6.782A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.368A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR E 205 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASN E 197 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG E 207 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER E 195 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER E 209 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU E 193 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER E 211 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS E 191 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG E 213 " --> pdb=" O VAL E 189 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2288 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: 2.68 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4294 1.34 - 1.46: 2991 1.46 - 1.57: 7181 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14606 Sorted by residual: bond pdb=" C1 MAN e 5 " pdb=" O5 MAN e 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 MAN e 4 " pdb=" O5 MAN e 4 " 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 d 5 " pdb=" O5 MAN d 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.45e+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 2.45e+00 bond pdb=" C1 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.41e+00 ... (remaining 14601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 18759 1.14 - 2.28: 848 2.28 - 3.42: 233 3.42 - 4.56: 34 4.56 - 5.71: 16 Bond angle restraints: 19890 Sorted by residual: angle pdb=" CA LYS E 279 " pdb=" C LYS E 279 " pdb=" N ALA E 280 " ideal model delta sigma weight residual 115.54 120.54 -5.00 1.52e+00 4.33e-01 1.08e+01 angle pdb=" CA LYS E 279 " pdb=" C LYS E 279 " pdb=" O LYS E 279 " ideal model delta sigma weight residual 121.60 117.90 3.70 1.21e+00 6.83e-01 9.36e+00 angle pdb=" C THR A 60 " pdb=" N MET A 61 " pdb=" CA MET A 61 " ideal model delta sigma weight residual 121.62 117.66 3.96 1.83e+00 2.99e-01 4.69e+00 angle pdb=" C TYR D 66 " pdb=" N TRP D 67 " pdb=" CA TRP D 67 " ideal model delta sigma weight residual 121.85 118.08 3.77 1.77e+00 3.19e-01 4.53e+00 angle pdb=" CA PRO D 276 " pdb=" C PRO D 276 " pdb=" O PRO D 276 " ideal model delta sigma weight residual 123.07 120.14 2.93 1.38e+00 5.25e-01 4.50e+00 ... (remaining 19885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 8733 21.02 - 42.04: 252 42.04 - 63.07: 38 63.07 - 84.09: 32 84.09 - 105.11: 21 Dihedral angle restraints: 9076 sinusoidal: 4107 harmonic: 4969 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 -176.40 105.11 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" O4 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C5 BMA c 3 " pdb=" O5 BMA c 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.19 104.90 1 3.00e+01 1.11e-03 1.34e+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 -176.06 104.77 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 9073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1986 0.059 - 0.118: 330 0.118 - 0.177: 24 0.177 - 0.236: 5 0.236 - 0.295: 7 Chirality restraints: 2352 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.68e+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 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2349 not shown) Planarity restraints: 2431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 275 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO D 276 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 276 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 276 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 275 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO B 276 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 275 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO A 276 " 0.051 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 2428 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1444 2.74 - 3.28: 14441 3.28 - 3.82: 24549 3.82 - 4.36: 28832 4.36 - 4.90: 49068 Nonbonded interactions: 118334 Sorted by model distance: nonbonded pdb=" O THR C 233 " pdb=" OG SER C 236 " model vdw 2.198 3.040 nonbonded pdb=" O ALA A 252 " pdb=" OG1 THR A 256 " model vdw 2.206 3.040 nonbonded pdb=" O THR E 233 " pdb=" OG SER E 236 " model vdw 2.218 3.040 nonbonded pdb=" O THR B 233 " pdb=" OG SER B 236 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR A 284 " pdb=" OD1 ASN A 439 " model vdw 2.254 3.040 ... (remaining 118329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 40 or resid 42 through 436 or resid 438 through \ 501)) selection = (chain 'B' and (resid 7 through 40 or resid 42 through 436 or resid 438 through \ 501)) selection = (chain 'C' and (resid 7 through 40 or resid 42 through 436 or resid 438 through \ 501)) selection = (chain 'D' and (resid 7 through 40 or resid 42 through 436 or resid 438 through \ 501)) selection = (chain 'E' and (resid 7 through 40 or resid 42 through 436 or resid 438 through \ 501)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.650 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 14651 Z= 0.257 Angle : 0.615 5.706 20020 Z= 0.300 Chirality : 0.046 0.295 2352 Planarity : 0.003 0.036 2416 Dihedral : 12.534 105.109 5879 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.81 % Allowed : 4.08 % Favored : 93.11 % 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: 1.95 (0.22), residues: 1676 helix: 2.82 (0.21), residues: 621 sheet: 0.48 (0.26), residues: 440 loop : 0.40 (0.28), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.017 0.002 TYR E 66 PHE 0.013 0.001 PHE C 63 TRP 0.006 0.001 TRP B 67 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00551 (14606) covalent geometry : angle 0.60776 (19890) SS BOND : bond 0.00112 ( 5) SS BOND : angle 0.52936 ( 10) hydrogen bonds : bond 0.10766 ( 723) hydrogen bonds : angle 4.89215 ( 2288) link_ALPHA1-3 : bond 0.00266 ( 5) link_ALPHA1-3 : angle 1.11154 ( 15) link_ALPHA1-6 : bond 0.00315 ( 5) link_ALPHA1-6 : angle 1.10776 ( 15) link_BETA1-4 : bond 0.00378 ( 15) link_BETA1-4 : angle 1.64066 ( 45) link_NAG-ASN : bond 0.00263 ( 15) link_NAG-ASN : angle 1.21864 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 SER cc_start: 0.9181 (t) cc_final: 0.8763 (p) REVERT: A 14 GLU cc_start: 0.9287 (tt0) cc_final: 0.9060 (pt0) REVERT: A 103 LYS cc_start: 0.8971 (tmtt) cc_final: 0.8661 (tmtt) REVERT: A 137 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8041 (mmm) REVERT: A 172 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8263 (t0) REVERT: A 215 LYS cc_start: 0.9103 (tttt) cc_final: 0.8775 (tmmt) REVERT: A 277 TYR cc_start: 0.7512 (p90) cc_final: 0.6824 (t80) REVERT: B 9 MET cc_start: 0.6373 (mtp) cc_final: 0.6064 (tmm) REVERT: B 61 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8077 (pp-130) REVERT: B 138 MET cc_start: 0.9243 (mtt) cc_final: 0.8949 (mtm) REVERT: B 155 GLU cc_start: 0.7591 (tt0) cc_final: 0.7341 (tt0) REVERT: C 9 MET cc_start: 0.8956 (mtp) cc_final: 0.8161 (pmm) REVERT: C 14 GLU cc_start: 0.9456 (tt0) cc_final: 0.9247 (tm-30) REVERT: C 55 MET cc_start: 0.8599 (mmt) cc_final: 0.8256 (mmm) REVERT: C 256 THR cc_start: 0.9338 (m) cc_final: 0.9110 (p) REVERT: D 87 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8839 (m) REVERT: D 90 GLN cc_start: 0.9200 (mt0) cc_final: 0.8842 (mp10) REVERT: D 112 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8784 (ttmm) REVERT: D 155 GLU cc_start: 0.8024 (tt0) cc_final: 0.7705 (tt0) REVERT: D 297 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9445 (mp) REVERT: D 306 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8388 (p90) REVERT: E 14 GLU cc_start: 0.9351 (tt0) cc_final: 0.9106 (pt0) REVERT: E 36 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8684 (m) REVERT: E 87 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7924 (p) REVERT: E 90 GLN cc_start: 0.9064 (mt0) cc_final: 0.8688 (mp10) REVERT: E 285 LEU cc_start: 0.9621 (mt) cc_final: 0.9390 (mp) outliers start: 42 outliers final: 14 residues processed: 285 average time/residue: 0.1473 time to fit residues: 58.9029 Evaluate side-chains 188 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN A 65 GLN ** B 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN C 54 ASN C 224 GLN D 41 ASN B D 119 HIS ** E 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN E 309 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.067132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.049131 restraints weight = 142851.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051927 restraints weight = 45547.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053803 restraints weight = 24476.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.055027 restraints weight = 16681.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.055768 restraints weight = 13118.252| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14651 Z= 0.135 Angle : 0.652 10.111 20020 Z= 0.325 Chirality : 0.046 0.273 2352 Planarity : 0.004 0.039 2416 Dihedral : 10.896 81.256 2744 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.67 % Allowed : 10.63 % Favored : 87.70 % 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: 1.80 (0.21), residues: 1676 helix: 2.42 (0.20), residues: 626 sheet: 0.84 (0.26), residues: 405 loop : 0.28 (0.27), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 269 TYR 0.018 0.002 TYR C 143 PHE 0.015 0.001 PHE B 200 TRP 0.008 0.001 TRP A 237 HIS 0.005 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00301 (14606) covalent geometry : angle 0.64234 (19890) SS BOND : bond 0.00150 ( 5) SS BOND : angle 0.64159 ( 10) hydrogen bonds : bond 0.03552 ( 723) hydrogen bonds : angle 4.11965 ( 2288) link_ALPHA1-3 : bond 0.00767 ( 5) link_ALPHA1-3 : angle 2.19335 ( 15) link_ALPHA1-6 : bond 0.00502 ( 5) link_ALPHA1-6 : angle 1.88156 ( 15) link_BETA1-4 : bond 0.00408 ( 15) link_BETA1-4 : angle 1.51095 ( 45) link_NAG-ASN : bond 0.00256 ( 15) link_NAG-ASN : angle 1.28885 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.522 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: A 9 MET cc_start: 0.9044 (mtt) cc_final: 0.8835 (mtt) REVERT: A 14 GLU cc_start: 0.9388 (tt0) cc_final: 0.9126 (pt0) REVERT: A 26 ARG cc_start: 0.8843 (ttp-110) cc_final: 0.8592 (mtm180) REVERT: A 65 GLN cc_start: 0.9345 (mt0) cc_final: 0.9011 (mp10) REVERT: A 103 LYS cc_start: 0.8979 (tmtt) cc_final: 0.8672 (tmtt) REVERT: A 277 TYR cc_start: 0.7538 (p90) cc_final: 0.6796 (t80) REVERT: A 283 MET cc_start: 0.9102 (mmm) cc_final: 0.8723 (mpp) REVERT: B 9 MET cc_start: 0.6146 (mtp) cc_final: 0.5695 (tmm) REVERT: B 61 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8245 (pp-130) REVERT: B 90 GLN cc_start: 0.8762 (mt0) cc_final: 0.8418 (mp10) REVERT: B 279 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8612 (mtpp) REVERT: C 9 MET cc_start: 0.9074 (mtp) cc_final: 0.8373 (pmm) REVERT: C 14 GLU cc_start: 0.9644 (tt0) cc_final: 0.9345 (tm-30) REVERT: C 18 LYS cc_start: 0.9608 (ptmm) cc_final: 0.9368 (ptmm) REVERT: C 55 MET cc_start: 0.8818 (mmt) cc_final: 0.8380 (mmt) REVERT: D 40 MET cc_start: 0.7725 (mpp) cc_final: 0.7352 (mpp) REVERT: D 112 LYS cc_start: 0.9257 (mtpp) cc_final: 0.8790 (ttmm) REVERT: D 115 MET cc_start: 0.8920 (ttt) cc_final: 0.8443 (ppp) REVERT: D 155 GLU cc_start: 0.8340 (tt0) cc_final: 0.7873 (tt0) REVERT: D 165 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8118 (mt-10) REVERT: D 283 MET cc_start: 0.9211 (mmm) cc_final: 0.8923 (mmm) REVERT: D 297 LEU cc_start: 0.9713 (mt) cc_final: 0.9495 (mp) REVERT: D 306 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8446 (p90) REVERT: E 14 GLU cc_start: 0.9451 (tt0) cc_final: 0.9142 (pt0) REVERT: E 232 ILE cc_start: 0.9677 (mm) cc_final: 0.9474 (tt) REVERT: E 283 MET cc_start: 0.9033 (mmm) cc_final: 0.8741 (mmm) outliers start: 25 outliers final: 10 residues processed: 218 average time/residue: 0.1382 time to fit residues: 42.9662 Evaluate side-chains 187 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 107 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 chunk 146 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.065886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048356 restraints weight = 118082.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050959 restraints weight = 41521.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.052690 restraints weight = 23315.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.053835 restraints weight = 16348.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.054571 restraints weight = 13064.846| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14651 Z= 0.172 Angle : 0.652 10.061 20020 Z= 0.322 Chirality : 0.045 0.198 2352 Planarity : 0.004 0.036 2416 Dihedral : 10.115 76.018 2722 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.74 % Allowed : 10.96 % Favored : 87.30 % 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: 1.62 (0.21), residues: 1676 helix: 2.23 (0.20), residues: 626 sheet: 0.88 (0.26), residues: 385 loop : 0.13 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 269 TYR 0.019 0.001 TYR C 143 PHE 0.015 0.001 PHE A 307 TRP 0.007 0.001 TRP E 67 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00387 (14606) covalent geometry : angle 0.64232 (19890) SS BOND : bond 0.00091 ( 5) SS BOND : angle 0.42466 ( 10) hydrogen bonds : bond 0.03341 ( 723) hydrogen bonds : angle 4.07281 ( 2288) link_ALPHA1-3 : bond 0.00936 ( 5) link_ALPHA1-3 : angle 1.98350 ( 15) link_ALPHA1-6 : bond 0.00679 ( 5) link_ALPHA1-6 : angle 1.99377 ( 15) link_BETA1-4 : bond 0.00298 ( 15) link_BETA1-4 : angle 1.46066 ( 45) link_NAG-ASN : bond 0.00145 ( 15) link_NAG-ASN : angle 1.42148 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.584 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 9 MET cc_start: 0.9078 (mtt) cc_final: 0.8871 (mtt) REVERT: A 14 GLU cc_start: 0.9380 (tt0) cc_final: 0.9120 (pt0) REVERT: A 65 GLN cc_start: 0.9328 (mt0) cc_final: 0.9041 (mp10) REVERT: A 103 LYS cc_start: 0.8977 (tmtt) cc_final: 0.8692 (tmtt) REVERT: A 182 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7320 (tm-30) REVERT: A 215 LYS cc_start: 0.9135 (tppt) cc_final: 0.8782 (mmtm) REVERT: A 277 TYR cc_start: 0.7601 (p90) cc_final: 0.6792 (t80) REVERT: A 283 MET cc_start: 0.9167 (mmm) cc_final: 0.8812 (tpp) REVERT: B 9 MET cc_start: 0.6206 (mtp) cc_final: 0.5693 (tmm) REVERT: B 55 MET cc_start: 0.9443 (mmt) cc_final: 0.9137 (tpp) REVERT: B 61 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8248 (pp-130) REVERT: B 87 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 153 GLU cc_start: 0.8329 (mp0) cc_final: 0.8088 (mp0) REVERT: B 279 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8591 (mtpp) REVERT: C 9 MET cc_start: 0.9107 (mtp) cc_final: 0.8345 (pmm) REVERT: C 14 GLU cc_start: 0.9628 (tt0) cc_final: 0.9342 (tm-30) REVERT: C 55 MET cc_start: 0.8815 (mmt) cc_final: 0.8350 (mmm) REVERT: C 79 LEU cc_start: 0.9238 (mp) cc_final: 0.8925 (pp) REVERT: C 261 MET cc_start: 0.9007 (tpp) cc_final: 0.8711 (ttm) REVERT: C 283 MET cc_start: 0.9467 (mmm) cc_final: 0.9265 (mmm) REVERT: D 18 LYS cc_start: 0.9554 (tttt) cc_final: 0.9353 (pttp) REVERT: D 40 MET cc_start: 0.7904 (mpp) cc_final: 0.7307 (mpp) REVERT: D 55 MET cc_start: 0.9045 (tpp) cc_final: 0.8378 (mmm) REVERT: D 61 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8497 (ptm) REVERT: D 90 GLN cc_start: 0.9236 (mt0) cc_final: 0.9014 (mp10) REVERT: D 112 LYS cc_start: 0.9283 (mtpp) cc_final: 0.8835 (ttmm) REVERT: D 138 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8450 (mmm) REVERT: D 155 GLU cc_start: 0.8382 (tt0) cc_final: 0.8042 (mm-30) REVERT: D 283 MET cc_start: 0.9246 (mmm) cc_final: 0.8872 (mmm) REVERT: D 297 LEU cc_start: 0.9713 (mt) cc_final: 0.9479 (mp) REVERT: D 306 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8452 (p90) REVERT: E 9 MET cc_start: 0.7819 (mtt) cc_final: 0.7145 (mtt) REVERT: E 14 GLU cc_start: 0.9474 (tt0) cc_final: 0.9184 (pt0) REVERT: E 61 MET cc_start: 0.9442 (ptp) cc_final: 0.9161 (ptp) REVERT: E 155 GLU cc_start: 0.7374 (tt0) cc_final: 0.6594 (tt0) REVERT: E 285 LEU cc_start: 0.9696 (mm) cc_final: 0.9428 (mp) outliers start: 26 outliers final: 13 residues processed: 203 average time/residue: 0.1452 time to fit residues: 41.8996 Evaluate side-chains 186 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 306 PHE 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 117 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.066856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.049070 restraints weight = 129538.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051797 restraints weight = 43615.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053604 restraints weight = 23912.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.054801 restraints weight = 16520.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.055569 restraints weight = 13079.153| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14651 Z= 0.128 Angle : 0.646 9.950 20020 Z= 0.319 Chirality : 0.045 0.211 2352 Planarity : 0.004 0.037 2416 Dihedral : 9.404 71.070 2722 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.40 % Allowed : 12.30 % Favored : 86.30 % 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: 1.58 (0.21), residues: 1676 helix: 2.03 (0.20), residues: 626 sheet: 0.98 (0.27), residues: 390 loop : 0.22 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 26 TYR 0.018 0.001 TYR C 143 PHE 0.016 0.001 PHE B 200 TRP 0.006 0.001 TRP E 67 HIS 0.006 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00291 (14606) covalent geometry : angle 0.63723 (19890) SS BOND : bond 0.00129 ( 5) SS BOND : angle 0.45923 ( 10) hydrogen bonds : bond 0.03187 ( 723) hydrogen bonds : angle 3.94870 ( 2288) link_ALPHA1-3 : bond 0.01033 ( 5) link_ALPHA1-3 : angle 2.03536 ( 15) link_ALPHA1-6 : bond 0.00795 ( 5) link_ALPHA1-6 : angle 2.00749 ( 15) link_BETA1-4 : bond 0.00369 ( 15) link_BETA1-4 : angle 1.35345 ( 45) link_NAG-ASN : bond 0.00188 ( 15) link_NAG-ASN : angle 1.29782 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.582 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: A 14 GLU cc_start: 0.9389 (tt0) cc_final: 0.9058 (pt0) REVERT: A 18 LYS cc_start: 0.9676 (tptp) cc_final: 0.9225 (ptpt) REVERT: A 65 GLN cc_start: 0.9285 (mt0) cc_final: 0.9054 (mp10) REVERT: A 215 LYS cc_start: 0.9103 (tppt) cc_final: 0.8769 (mmtm) REVERT: A 270 GLU cc_start: 0.8691 (tt0) cc_final: 0.8402 (pt0) REVERT: A 277 TYR cc_start: 0.7449 (p90) cc_final: 0.6812 (t80) REVERT: A 283 MET cc_start: 0.9204 (mmm) cc_final: 0.8901 (mmm) REVERT: B 9 MET cc_start: 0.5917 (mtp) cc_final: 0.5595 (tmm) REVERT: B 55 MET cc_start: 0.9450 (mmt) cc_final: 0.9167 (tpp) REVERT: B 61 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8198 (pp-130) REVERT: B 70 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8803 (mmmt) REVERT: B 90 GLN cc_start: 0.8222 (mp10) cc_final: 0.7978 (mp10) REVERT: B 99 LEU cc_start: 0.9266 (tp) cc_final: 0.9022 (tp) REVERT: C 9 MET cc_start: 0.9112 (mtp) cc_final: 0.8353 (pmm) REVERT: C 14 GLU cc_start: 0.9625 (tt0) cc_final: 0.9336 (tm-30) REVERT: C 49 MET cc_start: 0.8787 (ppp) cc_final: 0.8333 (ppp) REVERT: C 55 MET cc_start: 0.8815 (mmt) cc_final: 0.8319 (mmm) REVERT: C 79 LEU cc_start: 0.9230 (mp) cc_final: 0.9030 (pp) REVERT: C 147 GLU cc_start: 0.8739 (tt0) cc_final: 0.8174 (tp30) REVERT: C 153 GLU cc_start: 0.8729 (mm-30) cc_final: 0.7850 (mp0) REVERT: C 261 MET cc_start: 0.9001 (tpp) cc_final: 0.8661 (ttm) REVERT: D 55 MET cc_start: 0.9092 (tpp) cc_final: 0.8354 (mmm) REVERT: D 61 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8216 (ptm) REVERT: D 90 GLN cc_start: 0.9232 (mt0) cc_final: 0.9023 (mp10) REVERT: D 112 LYS cc_start: 0.9297 (mtpp) cc_final: 0.9088 (ttmm) REVERT: D 115 MET cc_start: 0.8930 (ttt) cc_final: 0.8523 (ppp) REVERT: D 138 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8433 (mmm) REVERT: D 283 MET cc_start: 0.9231 (mmm) cc_final: 0.8750 (mmm) REVERT: D 297 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9471 (mp) REVERT: D 306 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8437 (p90) REVERT: E 9 MET cc_start: 0.7668 (mtt) cc_final: 0.7446 (mmm) REVERT: E 14 GLU cc_start: 0.9478 (tt0) cc_final: 0.9189 (pt0) REVERT: E 61 MET cc_start: 0.9394 (ptp) cc_final: 0.9081 (ptp) REVERT: E 155 GLU cc_start: 0.7323 (tt0) cc_final: 0.6860 (tt0) outliers start: 21 outliers final: 11 residues processed: 196 average time/residue: 0.1561 time to fit residues: 42.9278 Evaluate side-chains 178 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 138 MET 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 63 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.065685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047943 restraints weight = 128648.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050571 restraints weight = 44573.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052327 restraints weight = 24876.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.053467 restraints weight = 17412.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.054192 restraints weight = 13950.178| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14651 Z= 0.183 Angle : 0.679 14.788 20020 Z= 0.331 Chirality : 0.046 0.222 2352 Planarity : 0.003 0.035 2416 Dihedral : 9.018 69.057 2718 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.01 % Allowed : 11.43 % Favored : 86.56 % 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: 1.51 (0.21), residues: 1676 helix: 1.97 (0.20), residues: 626 sheet: 0.68 (0.25), residues: 455 loop : 0.35 (0.28), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 26 TYR 0.019 0.001 TYR B 66 PHE 0.013 0.001 PHE E 63 TRP 0.007 0.001 TRP E 67 HIS 0.006 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00408 (14606) covalent geometry : angle 0.66925 (19890) SS BOND : bond 0.00040 ( 5) SS BOND : angle 0.40345 ( 10) hydrogen bonds : bond 0.03196 ( 723) hydrogen bonds : angle 3.98821 ( 2288) link_ALPHA1-3 : bond 0.01064 ( 5) link_ALPHA1-3 : angle 2.24312 ( 15) link_ALPHA1-6 : bond 0.00780 ( 5) link_ALPHA1-6 : angle 2.08699 ( 15) link_BETA1-4 : bond 0.00292 ( 15) link_BETA1-4 : angle 1.38979 ( 45) link_NAG-ASN : bond 0.00143 ( 15) link_NAG-ASN : angle 1.41042 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.541 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 14 GLU cc_start: 0.9390 (tt0) cc_final: 0.9119 (pt0) REVERT: A 65 GLN cc_start: 0.9323 (mt0) cc_final: 0.9036 (mp10) REVERT: A 115 MET cc_start: 0.8526 (ppp) cc_final: 0.8306 (ppp) REVERT: A 270 GLU cc_start: 0.8687 (tt0) cc_final: 0.8456 (pt0) REVERT: A 277 TYR cc_start: 0.7577 (p90) cc_final: 0.6816 (t80) REVERT: A 283 MET cc_start: 0.9205 (mmm) cc_final: 0.8880 (mmm) REVERT: B 9 MET cc_start: 0.5948 (mtp) cc_final: 0.5595 (tmm) REVERT: B 55 MET cc_start: 0.9498 (mmt) cc_final: 0.9174 (tpp) REVERT: B 61 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8211 (pp-130) REVERT: B 90 GLN cc_start: 0.8044 (mp10) cc_final: 0.7819 (mp10) REVERT: B 153 GLU cc_start: 0.8345 (mp0) cc_final: 0.8026 (mp0) REVERT: B 261 MET cc_start: 0.9183 (mmm) cc_final: 0.8944 (mmm) REVERT: C 9 MET cc_start: 0.9114 (mtp) cc_final: 0.8368 (pmm) REVERT: C 14 GLU cc_start: 0.9640 (tt0) cc_final: 0.9327 (tm-30) REVERT: C 18 LYS cc_start: 0.9543 (ptmm) cc_final: 0.9244 (ptmm) REVERT: C 49 MET cc_start: 0.8712 (ppp) cc_final: 0.8190 (ppp) REVERT: C 55 MET cc_start: 0.8861 (mmt) cc_final: 0.8381 (mmm) REVERT: C 79 LEU cc_start: 0.9169 (mp) cc_final: 0.8969 (pp) REVERT: C 153 GLU cc_start: 0.8718 (mm-30) cc_final: 0.7868 (mp0) REVERT: C 261 MET cc_start: 0.9052 (tpp) cc_final: 0.8638 (ttm) REVERT: C 274 LYS cc_start: 0.9171 (mmmt) cc_final: 0.8967 (mmpt) REVERT: D 55 MET cc_start: 0.9111 (tpp) cc_final: 0.8658 (mmm) REVERT: D 90 GLN cc_start: 0.9221 (mt0) cc_final: 0.8982 (mp10) REVERT: D 112 LYS cc_start: 0.9301 (mtpp) cc_final: 0.8857 (ttmm) REVERT: D 115 MET cc_start: 0.8967 (ttt) cc_final: 0.8447 (ppp) REVERT: D 138 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8508 (mmm) REVERT: D 283 MET cc_start: 0.9237 (mmm) cc_final: 0.8763 (mmm) REVERT: D 286 MET cc_start: 0.9028 (mmm) cc_final: 0.8789 (mmm) REVERT: D 297 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9458 (mp) REVERT: D 306 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8460 (p90) REVERT: E 9 MET cc_start: 0.7629 (mtt) cc_final: 0.7330 (mmm) REVERT: E 14 GLU cc_start: 0.9475 (tt0) cc_final: 0.9212 (pt0) REVERT: E 61 MET cc_start: 0.9400 (ptp) cc_final: 0.9100 (ptp) REVERT: E 270 GLU cc_start: 0.8782 (tt0) cc_final: 0.8523 (tt0) REVERT: E 282 ASP cc_start: 0.9094 (t70) cc_final: 0.8803 (t0) outliers start: 30 outliers final: 14 residues processed: 180 average time/residue: 0.1358 time to fit residues: 35.5079 Evaluate side-chains 171 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 PHE 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 82 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.066866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048779 restraints weight = 145689.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.051592 restraints weight = 45684.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053446 restraints weight = 24471.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.054670 restraints weight = 16736.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.055435 restraints weight = 13204.371| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14651 Z= 0.125 Angle : 0.666 13.041 20020 Z= 0.326 Chirality : 0.046 0.236 2352 Planarity : 0.003 0.033 2416 Dihedral : 8.542 65.819 2718 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.27 % Allowed : 11.97 % Favored : 86.76 % 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: 1.48 (0.21), residues: 1676 helix: 1.84 (0.20), residues: 626 sheet: 0.74 (0.25), residues: 455 loop : 0.39 (0.28), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 269 TYR 0.018 0.001 TYR B 66 PHE 0.014 0.001 PHE C 293 TRP 0.006 0.001 TRP A 92 HIS 0.006 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00285 (14606) covalent geometry : angle 0.65708 (19890) SS BOND : bond 0.00090 ( 5) SS BOND : angle 0.50344 ( 10) hydrogen bonds : bond 0.03188 ( 723) hydrogen bonds : angle 3.91910 ( 2288) link_ALPHA1-3 : bond 0.01088 ( 5) link_ALPHA1-3 : angle 2.14524 ( 15) link_ALPHA1-6 : bond 0.00914 ( 5) link_ALPHA1-6 : angle 1.96436 ( 15) link_BETA1-4 : bond 0.00349 ( 15) link_BETA1-4 : angle 1.30743 ( 45) link_NAG-ASN : bond 0.00179 ( 15) link_NAG-ASN : angle 1.30760 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.627 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 65 GLN cc_start: 0.9293 (mt0) cc_final: 0.8995 (mp10) REVERT: A 277 TYR cc_start: 0.7418 (p90) cc_final: 0.6809 (t80) REVERT: A 283 MET cc_start: 0.9173 (mmm) cc_final: 0.8837 (mmm) REVERT: B 9 MET cc_start: 0.5921 (mtp) cc_final: 0.5575 (tmm) REVERT: B 55 MET cc_start: 0.9480 (mmt) cc_final: 0.9136 (tpp) REVERT: B 61 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8182 (pp-130) REVERT: B 90 GLN cc_start: 0.8097 (mp10) cc_final: 0.7885 (mp10) REVERT: B 99 LEU cc_start: 0.9257 (tp) cc_final: 0.9009 (tp) REVERT: B 153 GLU cc_start: 0.8354 (mp0) cc_final: 0.7948 (mp0) REVERT: C 9 MET cc_start: 0.9104 (mtp) cc_final: 0.8353 (pmm) REVERT: C 14 GLU cc_start: 0.9629 (tt0) cc_final: 0.9311 (tm-30) REVERT: C 18 LYS cc_start: 0.9536 (ptmm) cc_final: 0.9253 (ptmm) REVERT: C 49 MET cc_start: 0.8756 (ppp) cc_final: 0.8371 (ppp) REVERT: C 55 MET cc_start: 0.8853 (mmt) cc_final: 0.8367 (mmm) REVERT: C 147 GLU cc_start: 0.8746 (tt0) cc_final: 0.8330 (tp30) REVERT: C 153 GLU cc_start: 0.8743 (mm-30) cc_final: 0.7869 (mp0) REVERT: C 261 MET cc_start: 0.9079 (tpp) cc_final: 0.8588 (ttm) REVERT: D 55 MET cc_start: 0.9167 (tpp) cc_final: 0.8755 (mmm) REVERT: D 90 GLN cc_start: 0.9193 (mt0) cc_final: 0.8964 (mp10) REVERT: D 112 LYS cc_start: 0.9298 (mtpp) cc_final: 0.9088 (ttmm) REVERT: D 115 MET cc_start: 0.8947 (ttt) cc_final: 0.8446 (ppp) REVERT: D 138 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8554 (mmm) REVERT: D 297 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9448 (mp) REVERT: D 306 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8443 (p90) REVERT: E 9 MET cc_start: 0.7701 (mtt) cc_final: 0.7437 (mmm) REVERT: E 14 GLU cc_start: 0.9482 (tt0) cc_final: 0.9201 (pt0) REVERT: E 61 MET cc_start: 0.9360 (ptp) cc_final: 0.9038 (ptp) REVERT: E 155 GLU cc_start: 0.7339 (tt0) cc_final: 0.6968 (tt0) REVERT: E 270 GLU cc_start: 0.8744 (tt0) cc_final: 0.8452 (tt0) outliers start: 19 outliers final: 10 residues processed: 173 average time/residue: 0.1376 time to fit residues: 34.4624 Evaluate side-chains 162 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 PHE 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 15 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 83 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.067058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049202 restraints weight = 144256.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.051979 restraints weight = 45976.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.053822 restraints weight = 24808.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.055032 restraints weight = 17014.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.055793 restraints weight = 13433.204| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14651 Z= 0.126 Angle : 0.688 15.461 20020 Z= 0.331 Chirality : 0.046 0.242 2352 Planarity : 0.003 0.039 2416 Dihedral : 8.089 62.811 2716 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.40 % Allowed : 12.23 % Favored : 86.36 % 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: 1.42 (0.21), residues: 1676 helix: 1.74 (0.20), residues: 626 sheet: 0.72 (0.25), residues: 455 loop : 0.43 (0.29), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 26 TYR 0.019 0.001 TYR B 66 PHE 0.013 0.001 PHE E 63 TRP 0.006 0.001 TRP B 67 HIS 0.007 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00286 (14606) covalent geometry : angle 0.68038 (19890) SS BOND : bond 0.00086 ( 5) SS BOND : angle 0.32856 ( 10) hydrogen bonds : bond 0.03158 ( 723) hydrogen bonds : angle 3.89411 ( 2288) link_ALPHA1-3 : bond 0.01080 ( 5) link_ALPHA1-3 : angle 2.12755 ( 15) link_ALPHA1-6 : bond 0.00975 ( 5) link_ALPHA1-6 : angle 1.92948 ( 15) link_BETA1-4 : bond 0.00358 ( 15) link_BETA1-4 : angle 1.26085 ( 45) link_NAG-ASN : bond 0.00157 ( 15) link_NAG-ASN : angle 1.33761 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.595 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 65 GLN cc_start: 0.9282 (mt0) cc_final: 0.8970 (mp10) REVERT: A 277 TYR cc_start: 0.7386 (p90) cc_final: 0.6832 (t80) REVERT: A 283 MET cc_start: 0.9157 (mmm) cc_final: 0.8876 (tpp) REVERT: B 9 MET cc_start: 0.5937 (mtp) cc_final: 0.5581 (tmm) REVERT: B 55 MET cc_start: 0.9460 (mmt) cc_final: 0.9113 (tpp) REVERT: B 61 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8175 (pp-130) REVERT: B 70 LYS cc_start: 0.9612 (mmmt) cc_final: 0.9324 (mmmt) REVERT: B 90 GLN cc_start: 0.8147 (mp10) cc_final: 0.7941 (mp10) REVERT: B 99 LEU cc_start: 0.9238 (tp) cc_final: 0.8991 (tp) REVERT: C 9 MET cc_start: 0.9128 (mtp) cc_final: 0.8445 (pmm) REVERT: C 14 GLU cc_start: 0.9622 (tt0) cc_final: 0.9397 (pt0) REVERT: C 49 MET cc_start: 0.8699 (ppp) cc_final: 0.8388 (ppp) REVERT: C 55 MET cc_start: 0.8843 (mmt) cc_final: 0.8423 (mmm) REVERT: C 147 GLU cc_start: 0.8750 (tt0) cc_final: 0.8333 (tp30) REVERT: C 153 GLU cc_start: 0.8754 (mm-30) cc_final: 0.7892 (mp0) REVERT: C 261 MET cc_start: 0.9093 (tpp) cc_final: 0.8601 (ttm) REVERT: D 55 MET cc_start: 0.9172 (tpp) cc_final: 0.8828 (mmm) REVERT: D 90 GLN cc_start: 0.9179 (mt0) cc_final: 0.8934 (mp10) REVERT: D 112 LYS cc_start: 0.9293 (mtpp) cc_final: 0.9091 (ttmm) REVERT: D 115 MET cc_start: 0.8923 (ttt) cc_final: 0.8498 (ppp) REVERT: D 138 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8578 (mmm) REVERT: D 270 GLU cc_start: 0.8840 (pt0) cc_final: 0.8535 (pp20) REVERT: D 283 MET cc_start: 0.9180 (mmm) cc_final: 0.8709 (mmm) REVERT: D 297 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9416 (mp) REVERT: D 306 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8416 (p90) REVERT: E 9 MET cc_start: 0.7753 (mtt) cc_final: 0.7503 (mmm) REVERT: E 14 GLU cc_start: 0.9473 (tt0) cc_final: 0.9167 (pt0) REVERT: E 155 GLU cc_start: 0.7480 (tt0) cc_final: 0.6806 (tt0) REVERT: E 274 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8890 (tppt) REVERT: E 286 MET cc_start: 0.8475 (ppp) cc_final: 0.8149 (ppp) outliers start: 21 outliers final: 11 residues processed: 176 average time/residue: 0.1418 time to fit residues: 35.8641 Evaluate side-chains 174 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 PHE 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 90 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.066948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049234 restraints weight = 125742.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051900 restraints weight = 43812.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.053663 restraints weight = 24542.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.054824 restraints weight = 17224.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055541 restraints weight = 13811.808| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14651 Z= 0.130 Angle : 0.675 13.170 20020 Z= 0.328 Chirality : 0.046 0.243 2352 Planarity : 0.003 0.035 2416 Dihedral : 7.764 60.540 2716 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.47 % Allowed : 12.23 % Favored : 86.30 % 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: 1.38 (0.21), residues: 1676 helix: 1.68 (0.20), residues: 626 sheet: 0.68 (0.25), residues: 455 loop : 0.44 (0.29), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 269 TYR 0.019 0.001 TYR B 66 PHE 0.021 0.001 PHE E 293 TRP 0.008 0.001 TRP B 67 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00296 (14606) covalent geometry : angle 0.66697 (19890) SS BOND : bond 0.00067 ( 5) SS BOND : angle 0.57986 ( 10) hydrogen bonds : bond 0.03210 ( 723) hydrogen bonds : angle 3.90413 ( 2288) link_ALPHA1-3 : bond 0.01073 ( 5) link_ALPHA1-3 : angle 2.16509 ( 15) link_ALPHA1-6 : bond 0.00992 ( 5) link_ALPHA1-6 : angle 1.88554 ( 15) link_BETA1-4 : bond 0.00371 ( 15) link_BETA1-4 : angle 1.26278 ( 45) link_NAG-ASN : bond 0.00136 ( 15) link_NAG-ASN : angle 1.35989 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.571 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 65 GLN cc_start: 0.9301 (mt0) cc_final: 0.8981 (mp10) REVERT: A 277 TYR cc_start: 0.7340 (p90) cc_final: 0.6830 (t80) REVERT: A 283 MET cc_start: 0.9159 (mmm) cc_final: 0.8910 (tpp) REVERT: B 9 MET cc_start: 0.5983 (mtp) cc_final: 0.5593 (tmm) REVERT: B 55 MET cc_start: 0.9456 (mmt) cc_final: 0.9100 (tpp) REVERT: B 61 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8173 (pp-130) REVERT: B 153 GLU cc_start: 0.8244 (mp0) cc_final: 0.7708 (mp0) REVERT: C 9 MET cc_start: 0.9096 (mtp) cc_final: 0.8364 (pmm) REVERT: C 14 GLU cc_start: 0.9658 (tt0) cc_final: 0.9340 (tm-30) REVERT: C 49 MET cc_start: 0.8768 (ppp) cc_final: 0.8420 (ppp) REVERT: C 55 MET cc_start: 0.8867 (mmt) cc_final: 0.8430 (mmm) REVERT: C 147 GLU cc_start: 0.8771 (tt0) cc_final: 0.8330 (tp30) REVERT: C 153 GLU cc_start: 0.8757 (mm-30) cc_final: 0.7908 (mp0) REVERT: C 261 MET cc_start: 0.9110 (tpp) cc_final: 0.8552 (ttm) REVERT: D 55 MET cc_start: 0.9195 (tpp) cc_final: 0.8856 (mmm) REVERT: D 90 GLN cc_start: 0.9177 (mt0) cc_final: 0.8930 (mp10) REVERT: D 112 LYS cc_start: 0.9295 (mtpp) cc_final: 0.9091 (ttmm) REVERT: D 115 MET cc_start: 0.8943 (ttt) cc_final: 0.8504 (ppp) REVERT: D 138 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8561 (mmm) REVERT: D 270 GLU cc_start: 0.8949 (pt0) cc_final: 0.8620 (pp20) REVERT: D 283 MET cc_start: 0.9171 (mmm) cc_final: 0.8687 (mmm) REVERT: D 297 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9413 (mp) REVERT: D 306 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8422 (p90) REVERT: E 9 MET cc_start: 0.7742 (mtt) cc_final: 0.7482 (mmm) REVERT: E 14 GLU cc_start: 0.9478 (tt0) cc_final: 0.9173 (pt0) REVERT: E 155 GLU cc_start: 0.7423 (tt0) cc_final: 0.6715 (tt0) REVERT: E 274 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8934 (tppt) REVERT: E 283 MET cc_start: 0.9033 (mmm) cc_final: 0.8475 (mmm) REVERT: E 286 MET cc_start: 0.8495 (ppp) cc_final: 0.8210 (ppp) outliers start: 22 outliers final: 16 residues processed: 178 average time/residue: 0.1369 time to fit residues: 35.5260 Evaluate side-chains 174 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 244 TYR 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 46 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 162 optimal weight: 0.2980 chunk 52 optimal weight: 0.0010 chunk 25 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.067604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.049888 restraints weight = 125699.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.052599 restraints weight = 43212.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.054417 restraints weight = 23984.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.055594 restraints weight = 16715.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.056342 restraints weight = 13359.998| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14651 Z= 0.119 Angle : 0.691 13.307 20020 Z= 0.334 Chirality : 0.046 0.246 2352 Planarity : 0.003 0.041 2416 Dihedral : 7.346 57.396 2716 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.14 % Allowed : 13.03 % Favored : 85.83 % 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: 1.39 (0.21), residues: 1676 helix: 1.64 (0.20), residues: 626 sheet: 0.71 (0.25), residues: 455 loop : 0.49 (0.29), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 269 TYR 0.019 0.001 TYR B 66 PHE 0.017 0.001 PHE E 293 TRP 0.009 0.001 TRP A 92 HIS 0.007 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00271 (14606) covalent geometry : angle 0.68393 (19890) SS BOND : bond 0.00162 ( 5) SS BOND : angle 0.49190 ( 10) hydrogen bonds : bond 0.03141 ( 723) hydrogen bonds : angle 3.89504 ( 2288) link_ALPHA1-3 : bond 0.01153 ( 5) link_ALPHA1-3 : angle 2.11166 ( 15) link_ALPHA1-6 : bond 0.01058 ( 5) link_ALPHA1-6 : angle 1.76503 ( 15) link_BETA1-4 : bond 0.00399 ( 15) link_BETA1-4 : angle 1.20235 ( 45) link_NAG-ASN : bond 0.00180 ( 15) link_NAG-ASN : angle 1.32100 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.584 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 65 GLN cc_start: 0.9255 (mt0) cc_final: 0.8801 (mp10) REVERT: A 224 GLN cc_start: 0.8867 (pp30) cc_final: 0.8601 (pp30) REVERT: A 277 TYR cc_start: 0.7283 (p90) cc_final: 0.6793 (t80) REVERT: A 283 MET cc_start: 0.9135 (mmm) cc_final: 0.8886 (tpp) REVERT: B 9 MET cc_start: 0.5922 (mtp) cc_final: 0.5545 (tmm) REVERT: B 40 MET cc_start: 0.9098 (mmm) cc_final: 0.8850 (tpp) REVERT: B 55 MET cc_start: 0.9423 (mmt) cc_final: 0.9079 (tpp) REVERT: B 61 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8144 (pp-130) REVERT: B 153 GLU cc_start: 0.7986 (mp0) cc_final: 0.7627 (mp0) REVERT: B 270 GLU cc_start: 0.8532 (pp20) cc_final: 0.8331 (pp20) REVERT: C 9 MET cc_start: 0.9073 (mtp) cc_final: 0.8581 (pmm) REVERT: C 14 GLU cc_start: 0.9668 (tt0) cc_final: 0.9411 (pt0) REVERT: C 49 MET cc_start: 0.8770 (ppp) cc_final: 0.8477 (ppp) REVERT: C 55 MET cc_start: 0.8854 (mmt) cc_final: 0.8404 (mmm) REVERT: C 147 GLU cc_start: 0.8755 (tt0) cc_final: 0.8341 (tp30) REVERT: C 153 GLU cc_start: 0.8779 (mm-30) cc_final: 0.7950 (mp0) REVERT: C 261 MET cc_start: 0.9089 (tpp) cc_final: 0.8543 (ttm) REVERT: D 18 LYS cc_start: 0.9544 (tttt) cc_final: 0.9329 (pttp) REVERT: D 55 MET cc_start: 0.9171 (tpp) cc_final: 0.8762 (mmm) REVERT: D 90 GLN cc_start: 0.9178 (mt0) cc_final: 0.8939 (mp10) REVERT: D 115 MET cc_start: 0.8910 (ttt) cc_final: 0.8530 (ppp) REVERT: D 270 GLU cc_start: 0.8739 (pt0) cc_final: 0.8478 (pp20) REVERT: D 283 MET cc_start: 0.9145 (mmm) cc_final: 0.8658 (mmm) REVERT: D 297 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9457 (mp) REVERT: D 306 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8419 (p90) REVERT: E 9 MET cc_start: 0.7705 (mtt) cc_final: 0.7458 (mmm) REVERT: E 14 GLU cc_start: 0.9494 (tt0) cc_final: 0.9210 (pt0) REVERT: E 155 GLU cc_start: 0.7417 (tt0) cc_final: 0.6653 (tt0) REVERT: E 274 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8885 (tppt) REVERT: E 283 MET cc_start: 0.8995 (mmm) cc_final: 0.8440 (tpt) REVERT: E 286 MET cc_start: 0.8460 (ppp) cc_final: 0.8126 (ppp) outliers start: 17 outliers final: 11 residues processed: 176 average time/residue: 0.1381 time to fit residues: 35.0964 Evaluate side-chains 165 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 244 TYR 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 106 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.065944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.048684 restraints weight = 106564.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.051188 restraints weight = 40461.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052850 restraints weight = 23381.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.053921 restraints weight = 16726.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.054620 restraints weight = 13581.210| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14651 Z= 0.202 Angle : 0.723 12.269 20020 Z= 0.352 Chirality : 0.046 0.254 2352 Planarity : 0.003 0.040 2416 Dihedral : 7.366 59.291 2715 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.14 % Allowed : 13.44 % Favored : 85.43 % 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: 1.32 (0.21), residues: 1676 helix: 1.60 (0.20), residues: 626 sheet: 0.65 (0.25), residues: 455 loop : 0.45 (0.29), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 269 TYR 0.020 0.001 TYR B 66 PHE 0.022 0.001 PHE E 289 TRP 0.013 0.001 TRP B 67 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00452 (14606) covalent geometry : angle 0.71466 (19890) SS BOND : bond 0.00136 ( 5) SS BOND : angle 0.68925 ( 10) hydrogen bonds : bond 0.03283 ( 723) hydrogen bonds : angle 4.03864 ( 2288) link_ALPHA1-3 : bond 0.00955 ( 5) link_ALPHA1-3 : angle 2.25422 ( 15) link_ALPHA1-6 : bond 0.00983 ( 5) link_ALPHA1-6 : angle 1.87810 ( 15) link_BETA1-4 : bond 0.00361 ( 15) link_BETA1-4 : angle 1.32559 ( 45) link_NAG-ASN : bond 0.00135 ( 15) link_NAG-ASN : angle 1.45278 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.532 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 65 GLN cc_start: 0.9329 (mt0) cc_final: 0.8967 (mp10) REVERT: A 277 TYR cc_start: 0.7402 (p90) cc_final: 0.6822 (t80) REVERT: A 283 MET cc_start: 0.9182 (mmm) cc_final: 0.8931 (tpp) REVERT: B 9 MET cc_start: 0.5928 (mtp) cc_final: 0.5563 (tmm) REVERT: B 40 MET cc_start: 0.9163 (mmm) cc_final: 0.8840 (tpp) REVERT: B 55 MET cc_start: 0.9502 (mmt) cc_final: 0.9243 (mmt) REVERT: B 61 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8190 (pp-130) REVERT: B 155 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8099 (mp0) REVERT: B 270 GLU cc_start: 0.8675 (pp20) cc_final: 0.8403 (pp20) REVERT: C 9 MET cc_start: 0.9107 (mtp) cc_final: 0.8617 (pmm) REVERT: C 14 GLU cc_start: 0.9661 (tt0) cc_final: 0.9343 (tm-30) REVERT: C 55 MET cc_start: 0.8889 (mmt) cc_final: 0.8445 (mmm) REVERT: C 147 GLU cc_start: 0.8714 (tt0) cc_final: 0.8281 (tp30) REVERT: C 153 GLU cc_start: 0.8739 (mm-30) cc_final: 0.7922 (mp0) REVERT: D 55 MET cc_start: 0.9151 (tpp) cc_final: 0.8770 (mmm) REVERT: D 90 GLN cc_start: 0.9058 (mt0) cc_final: 0.8629 (mp10) REVERT: D 112 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8579 (tttm) REVERT: D 115 MET cc_start: 0.8992 (ttt) cc_final: 0.8511 (ppp) REVERT: D 283 MET cc_start: 0.9164 (mmm) cc_final: 0.8668 (mmm) REVERT: D 297 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9389 (mp) REVERT: D 306 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8425 (p90) REVERT: E 9 MET cc_start: 0.7731 (mtt) cc_final: 0.7454 (mmm) REVERT: E 14 GLU cc_start: 0.9503 (tt0) cc_final: 0.9230 (pt0) REVERT: E 155 GLU cc_start: 0.7513 (tt0) cc_final: 0.7285 (tt0) REVERT: E 274 LYS cc_start: 0.9228 (mmmt) cc_final: 0.9024 (tppt) REVERT: E 286 MET cc_start: 0.8460 (ppp) cc_final: 0.8181 (ppp) outliers start: 17 outliers final: 10 residues processed: 165 average time/residue: 0.1381 time to fit residues: 32.9979 Evaluate side-chains 162 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 PHE 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 39 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.066469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048605 restraints weight = 150446.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051387 restraints weight = 46406.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.053235 restraints weight = 24780.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.054450 restraints weight = 16878.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.055216 restraints weight = 13297.952| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14651 Z= 0.144 Angle : 0.716 12.843 20020 Z= 0.345 Chirality : 0.046 0.237 2352 Planarity : 0.003 0.040 2416 Dihedral : 7.156 59.215 2715 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.94 % Allowed : 13.77 % Favored : 85.29 % 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: 1.29 (0.21), residues: 1676 helix: 1.58 (0.20), residues: 626 sheet: 0.64 (0.25), residues: 455 loop : 0.43 (0.29), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 269 TYR 0.019 0.001 TYR B 66 PHE 0.017 0.001 PHE E 293 TRP 0.009 0.001 TRP B 67 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00328 (14606) covalent geometry : angle 0.70850 (19890) SS BOND : bond 0.00140 ( 5) SS BOND : angle 0.62948 ( 10) hydrogen bonds : bond 0.03221 ( 723) hydrogen bonds : angle 3.99461 ( 2288) link_ALPHA1-3 : bond 0.00993 ( 5) link_ALPHA1-3 : angle 2.09386 ( 15) link_ALPHA1-6 : bond 0.01053 ( 5) link_ALPHA1-6 : angle 1.74960 ( 15) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.28834 ( 45) link_NAG-ASN : bond 0.00121 ( 15) link_NAG-ASN : angle 1.38914 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.98 seconds wall clock time: 46 minutes 23.50 seconds (2783.50 seconds total)