Starting phenix.real_space_refine on Fri Jul 3 09:23:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kf9_22847/07_2026/7kf9_22847.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kf9_22847/07_2026/7kf9_22847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2026/7kf9_22847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2026/7kf9_22847.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2026/7kf9_22847.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2026/7kf9_22847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2026/7kf9_22847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2026/7kf9_22847.map" } resolution = 4.4 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= 0.001 sd= 0.072 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 42 5.16 5 C 8331 2.51 5 N 2214 2.21 5 O 2574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13161 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "C" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "F" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "B" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "E" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "M" 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 chiralities: 5 Chain: "N" 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 chiralities: 5 Chain: "O" 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 chiralities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.44, per 1000 atoms: 0.19 Number of scatterers: 13161 At special positions: 0 Unit cell: (148.35, 148.35, 106.95, 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 42 16.00 O 2574 8.00 N 2214 7.00 C 8331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.02 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 M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 257 " " NAG A 402 " - " ASN A 268 " " NAG A 403 " - " ASN A 228 " " NAG B 401 " - " ASN B 257 " " NAG B 402 " - " ASN B 268 " " NAG B 403 " - " ASN B 228 " " NAG C 401 " - " ASN C 257 " " NAG C 402 " - " ASN C 268 " " NAG C 403 " - " ASN C 228 " " NAG M 1 " - " ASN D 563 " " NAG N 1 " - " ASN F 563 " " NAG O 1 " - " ASN E 563 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 535.4 milliseconds 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 27 sheets defined 16.8% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.787A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'D' and resid 528 through 532 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.033A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.785A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'F' and resid 528 through 532 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.033A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 84 removed outlier: 3.787A pdb=" N LYS B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'E' and resid 528 through 532 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.032A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.217A pdb=" N TYR G 35 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP G 36 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE G 52 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP G 38 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.755A pdb=" N VAL G 120 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 45 removed outlier: 5.260A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.553A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 14.582A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 98 removed outlier: 8.433A pdb=" N ALA A 101 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 65 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLU A 103 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY A 67 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA7, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA J 10 " --> pdb=" O THR J 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA J 10 " --> pdb=" O THR J 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AB1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.215A pdb=" N TYR I 35 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP I 36 " --> pdb=" O PHE I 52 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 52 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP I 38 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.757A pdb=" N VAL I 120 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.259A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.553A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 14.583A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 98 removed outlier: 5.968A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.216A pdb=" N TYR H 35 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP H 36 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.756A pdb=" N VAL H 120 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 43 through 45 removed outlier: 5.260A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.554A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 11.527A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.583A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.545A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.968A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA K 10 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA K 10 " --> pdb=" O THR K 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 17 through 23 516 hydrogen bonds defined for protein. 1263 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: 1.80 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2727 1.32 - 1.46: 4619 1.46 - 1.59: 6025 1.59 - 1.73: 48 1.73 - 1.87: 45 Bond restraints: 13464 Sorted by residual: bond pdb=" CB HIS A 154 " pdb=" CG HIS A 154 " ideal model delta sigma weight residual 1.497 1.383 0.114 1.40e-02 5.10e+03 6.68e+01 bond pdb=" CB HIS B 154 " pdb=" CG HIS B 154 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.57e+01 bond pdb=" CB HIS C 154 " pdb=" CG HIS C 154 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.47e+01 bond pdb=" CB LEU L 111 " pdb=" CG LEU L 111 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" CB LEU J 111 " pdb=" CG LEU J 111 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.45e+01 ... (remaining 13459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 16440 3.01 - 6.01: 1660 6.01 - 9.02: 192 9.02 - 12.02: 8 12.02 - 15.03: 3 Bond angle restraints: 18303 Sorted by residual: angle pdb=" C ALA C 125 " pdb=" N PRO C 126 " pdb=" CA PRO C 126 " ideal model delta sigma weight residual 120.21 128.35 -8.14 9.60e-01 1.09e+00 7.19e+01 angle pdb=" C ALA B 125 " pdb=" N PRO B 126 " pdb=" CA PRO B 126 " ideal model delta sigma weight residual 120.21 128.24 -8.03 9.60e-01 1.09e+00 7.00e+01 angle pdb=" C ALA A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 126 " ideal model delta sigma weight residual 120.21 128.20 -7.99 9.60e-01 1.09e+00 6.93e+01 angle pdb=" C GLY D 536 " pdb=" N PRO D 537 " pdb=" CA PRO D 537 " ideal model delta sigma weight residual 120.03 127.22 -7.19 9.90e-01 1.02e+00 5.27e+01 angle pdb=" C GLY F 536 " pdb=" N PRO F 537 " pdb=" CA PRO F 537 " ideal model delta sigma weight residual 120.03 127.19 -7.16 9.90e-01 1.02e+00 5.23e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7416 17.92 - 35.83: 180 35.83 - 53.75: 60 53.75 - 71.66: 15 71.66 - 89.58: 21 Dihedral angle restraints: 7692 sinusoidal: 2988 harmonic: 4704 Sorted by residual: dihedral pdb=" CA PHE H 34 " pdb=" C PHE H 34 " pdb=" N TYR H 35 " pdb=" CA TYR H 35 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE I 34 " pdb=" C PHE I 34 " pdb=" N TYR I 35 " pdb=" CA TYR I 35 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE G 34 " pdb=" C PHE G 34 " pdb=" N TYR G 35 " pdb=" CA TYR G 35 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 7689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1374 0.097 - 0.194: 515 0.194 - 0.291: 138 0.291 - 0.388: 42 0.388 - 0.484: 22 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 ... (remaining 2088 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 113 " 0.070 2.00e-02 2.50e+03 3.62e-02 2.62e+01 pdb=" CG TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR I 113 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR I 113 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR I 113 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR I 113 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 113 " 0.070 2.00e-02 2.50e+03 3.59e-02 2.58e+01 pdb=" CG TYR H 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR H 113 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR H 113 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR H 113 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR H 113 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR H 113 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR H 113 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 113 " -0.070 2.00e-02 2.50e+03 3.59e-02 2.57e+01 pdb=" CG TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR G 113 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR G 113 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 113 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR G 113 " -0.044 2.00e-02 2.50e+03 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 6637 2.96 - 3.44: 12335 3.44 - 3.93: 23579 3.93 - 4.41: 27520 4.41 - 4.90: 42979 Nonbonded interactions: 113050 Sorted by model distance: nonbonded pdb=" N ASP K 61 " pdb=" OD1 ASP K 61 " model vdw 2.470 3.120 nonbonded pdb=" N ASP J 61 " pdb=" OD1 ASP J 61 " model vdw 2.471 3.120 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.471 3.120 nonbonded pdb=" N THR B 249 " pdb=" O THR B 249 " model vdw 2.480 2.496 nonbonded pdb=" N THR C 249 " pdb=" O THR C 249 " model vdw 2.480 2.496 ... (remaining 113045 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: 0.04 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'E' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.022 0.148 13497 Z= 1.155 Angle : 1.890 15.027 18393 Z= 1.248 Chirality : 0.117 0.484 2091 Planarity : 0.009 0.053 2313 Dihedral : 10.634 89.579 4683 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.37 (0.19), residues: 1626 helix: -0.35 (0.29), residues: 195 sheet: -0.12 (0.23), residues: 489 loop : 0.79 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 85 TYR 0.070 0.012 TYR I 113 PHE 0.038 0.006 PHE H 80 TRP 0.053 0.011 TRP H 49 HIS 0.008 0.003 HIS E 549 Details of bonding type rmsd/Z covalent geometry : bond 0.02149 / 1.14 (13464) covalent geometry : angle 1.88005 / 1.25 (18303) SS BOND : bond 0.00771 / 0.42 ( 9) SS BOND : angle 2.02885 / 1.36 ( 18) hydrogen bonds : bond 0.16680 / 10.75 ( 489) hydrogen bonds : angle 8.52206 / 6.03 ( 1263) link_ALPHA1-3 : bond 0.08406 / 4.22 ( 3) link_ALPHA1-3 : angle 4.44207 / 2.66 ( 9) link_ALPHA1-6 : bond 0.05315 / 2.67 ( 3) link_ALPHA1-6 : angle 2.77680 / 1.67 ( 9) link_BETA1-4 : bond 0.07659 / 3.92 ( 6) link_BETA1-4 : angle 5.58955 / 3.53 ( 18) link_NAG-ASN : bond 0.08402 / 5.06 ( 12) link_NAG-ASN : angle 2.04855 / 1.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 0.536 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: G 118 MET cc_start: 0.8740 (ttt) cc_final: 0.7477 (tmm) REVERT: A 171 TYR cc_start: 0.9332 (m-80) cc_final: 0.9104 (m-80) REVERT: A 237 ASP cc_start: 0.9043 (t0) cc_final: 0.8731 (m-30) REVERT: J 35 ASP cc_start: 0.9207 (m-30) cc_final: 0.8372 (p0) REVERT: J 53 ASP cc_start: 0.8865 (p0) cc_final: 0.7837 (t0) REVERT: I 118 MET cc_start: 0.8656 (ttt) cc_final: 0.7637 (tmm) REVERT: C 99 TYR cc_start: 0.7360 (m-80) cc_final: 0.6748 (m-80) REVERT: C 109 TYR cc_start: 0.8670 (m-80) cc_final: 0.8435 (m-10) REVERT: C 237 ASP cc_start: 0.9032 (t0) cc_final: 0.8662 (m-30) REVERT: L 35 ASP cc_start: 0.9168 (m-30) cc_final: 0.8444 (p0) REVERT: L 53 ASP cc_start: 0.8886 (p0) cc_final: 0.7881 (t0) REVERT: H 118 MET cc_start: 0.8807 (ttt) cc_final: 0.7805 (tmm) REVERT: B 127 ASP cc_start: 0.9447 (m-30) cc_final: 0.9211 (t0) REVERT: B 237 ASP cc_start: 0.9006 (t0) cc_final: 0.8605 (m-30) REVERT: K 35 ASP cc_start: 0.9210 (m-30) cc_final: 0.8461 (p0) REVERT: K 53 ASP cc_start: 0.8913 (p0) cc_final: 0.7985 (t0) outliers start: 6 outliers final: 0 residues processed: 227 average time/residue: 0.1030 time to fit residues: 33.6830 Evaluate side-chains 75 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN C 107 ASN L 28 ASN B 107 ASN K 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.036314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.030115 restraints weight = 148892.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.031280 restraints weight = 80463.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.032127 restraints weight = 51879.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.032715 restraints weight = 37054.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.033161 restraints weight = 28525.677| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13497 Z= 0.299 Angle : 0.845 7.438 18393 Z= 0.447 Chirality : 0.048 0.227 2091 Planarity : 0.005 0.044 2313 Dihedral : 6.330 30.385 1806 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.91 % Favored : 97.91 % Rotamer: Outliers : 0.22 % Allowed : 2.15 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: 0.05 (0.20), residues: 1626 helix: -0.32 (0.31), residues: 195 sheet: -0.34 (0.20), residues: 606 loop : 0.66 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 266 TYR 0.017 0.002 TYR I 113 PHE 0.033 0.003 PHE A 252 TRP 0.021 0.003 TRP L 100 HIS 0.005 0.001 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.30 (13464) covalent geometry : angle 0.82978 / 0.44 (18303) SS BOND : bond 0.01122 / 0.65 ( 9) SS BOND : angle 2.53677 / 1.50 ( 18) hydrogen bonds : bond 0.06055 / 4.02 ( 489) hydrogen bonds : angle 7.37620 / 5.16 ( 1263) link_ALPHA1-3 : bond 0.00328 / 0.16 ( 3) link_ALPHA1-3 : angle 2.34934 / 1.54 ( 9) link_ALPHA1-6 : bond 0.00276 / 0.14 ( 3) link_ALPHA1-6 : angle 2.22399 / 1.38 ( 9) link_BETA1-4 : bond 0.00694 / 0.38 ( 6) link_BETA1-4 : angle 3.11828 / 1.95 ( 18) link_NAG-ASN : bond 0.00856 / 0.52 ( 12) link_NAG-ASN : angle 1.90577 / 1.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.406 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: G 118 MET cc_start: 0.8762 (ttt) cc_final: 0.8256 (tmm) REVERT: A 171 TYR cc_start: 0.9243 (m-80) cc_final: 0.8664 (m-80) REVERT: A 237 ASP cc_start: 0.9049 (t0) cc_final: 0.8801 (m-30) REVERT: J 35 ASP cc_start: 0.9201 (m-30) cc_final: 0.8998 (m-30) REVERT: I 118 MET cc_start: 0.8651 (ttt) cc_final: 0.8089 (tmm) REVERT: C 161 LEU cc_start: 0.9275 (mt) cc_final: 0.9070 (mt) REVERT: C 171 TYR cc_start: 0.9421 (m-80) cc_final: 0.9130 (m-80) REVERT: C 237 ASP cc_start: 0.9090 (t0) cc_final: 0.8829 (m-30) REVERT: C 273 LEU cc_start: 0.9130 (mt) cc_final: 0.8924 (mt) REVERT: L 61 ASP cc_start: 0.9542 (p0) cc_final: 0.9335 (p0) REVERT: L 74 LEU cc_start: 0.9305 (tt) cc_final: 0.9086 (pp) REVERT: H 118 MET cc_start: 0.8654 (ttt) cc_final: 0.8402 (tmm) REVERT: B 109 TYR cc_start: 0.8665 (m-80) cc_final: 0.8369 (m-10) REVERT: B 171 TYR cc_start: 0.9340 (m-80) cc_final: 0.8928 (m-80) REVERT: B 237 ASP cc_start: 0.9028 (t0) cc_final: 0.8698 (m-30) REVERT: B 273 LEU cc_start: 0.9120 (mt) cc_final: 0.8848 (mt) REVERT: K 74 LEU cc_start: 0.9271 (tt) cc_final: 0.9067 (pp) outliers start: 3 outliers final: 0 residues processed: 120 average time/residue: 0.0984 time to fit residues: 17.5062 Evaluate side-chains 66 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 69 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.036558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.030294 restraints weight = 148311.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.031474 restraints weight = 80286.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.032329 restraints weight = 51706.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.032916 restraints weight = 37065.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.033365 restraints weight = 28700.140| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13497 Z= 0.156 Angle : 0.663 7.453 18393 Z= 0.351 Chirality : 0.045 0.192 2091 Planarity : 0.004 0.032 2313 Dihedral : 5.757 27.613 1806 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.20 (0.21), residues: 1626 helix: -0.14 (0.33), residues: 198 sheet: -0.25 (0.20), residues: 636 loop : 0.79 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 559 TYR 0.021 0.002 TYR A 99 PHE 0.017 0.002 PHE G 80 TRP 0.016 0.002 TRP G 36 HIS 0.002 0.001 HIS D 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (13464) covalent geometry : angle 0.65236 / 0.35 (18303) SS BOND : bond 0.00502 / 0.28 ( 9) SS BOND : angle 2.04706 / 1.23 ( 18) hydrogen bonds : bond 0.04937 / 3.26 ( 489) hydrogen bonds : angle 6.78555 / 4.74 ( 1263) link_ALPHA1-3 : bond 0.00517 / 0.26 ( 3) link_ALPHA1-3 : angle 1.45299 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00269 / 0.13 ( 3) link_ALPHA1-6 : angle 1.44398 / 0.89 ( 9) link_BETA1-4 : bond 0.00696 / 0.36 ( 6) link_BETA1-4 : angle 2.66500 / 1.70 ( 18) link_NAG-ASN : bond 0.00619 / 0.38 ( 12) link_NAG-ASN : angle 1.24170 / 0.83 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.488 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: G 118 MET cc_start: 0.8789 (ttt) cc_final: 0.8077 (tmm) REVERT: A 171 TYR cc_start: 0.9229 (m-80) cc_final: 0.8619 (m-80) REVERT: A 237 ASP cc_start: 0.9184 (t0) cc_final: 0.8862 (m-30) REVERT: A 273 LEU cc_start: 0.8875 (mt) cc_final: 0.8624 (mt) REVERT: D 548 MET cc_start: 0.7019 (mmt) cc_final: 0.6654 (mmt) REVERT: I 118 MET cc_start: 0.8714 (ttt) cc_final: 0.7950 (tmm) REVERT: C 171 TYR cc_start: 0.9379 (m-80) cc_final: 0.8963 (m-80) REVERT: C 237 ASP cc_start: 0.9116 (t0) cc_final: 0.8779 (m-30) REVERT: C 273 LEU cc_start: 0.9057 (mt) cc_final: 0.8826 (mt) REVERT: L 35 ASP cc_start: 0.9397 (m-30) cc_final: 0.8694 (p0) REVERT: H 118 MET cc_start: 0.8753 (ttt) cc_final: 0.8036 (tmm) REVERT: B 171 TYR cc_start: 0.9303 (m-80) cc_final: 0.8903 (m-80) REVERT: B 237 ASP cc_start: 0.9110 (t0) cc_final: 0.8727 (m-30) REVERT: B 273 LEU cc_start: 0.8994 (mt) cc_final: 0.8662 (mt) REVERT: K 35 ASP cc_start: 0.9297 (m-30) cc_final: 0.8687 (p0) REVERT: K 74 LEU cc_start: 0.9293 (tt) cc_final: 0.9042 (tt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1071 time to fit residues: 16.8780 Evaluate side-chains 71 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 161 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.035716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.029509 restraints weight = 149424.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.030617 restraints weight = 82306.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.031425 restraints weight = 53780.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.031997 restraints weight = 38821.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.032429 restraints weight = 30212.400| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13497 Z= 0.171 Angle : 0.662 9.948 18393 Z= 0.343 Chirality : 0.045 0.263 2091 Planarity : 0.004 0.032 2313 Dihedral : 5.666 25.800 1806 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.14 (0.21), residues: 1626 helix: -0.12 (0.33), residues: 195 sheet: -0.20 (0.20), residues: 633 loop : 0.64 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 99 TYR 0.022 0.002 TYR B 109 PHE 0.018 0.002 PHE I 80 TRP 0.044 0.003 TRP G 121 HIS 0.007 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (13464) covalent geometry : angle 0.65181 / 0.34 (18303) SS BOND : bond 0.00676 / 0.38 ( 9) SS BOND : angle 2.18054 / 1.30 ( 18) hydrogen bonds : bond 0.04548 / 2.99 ( 489) hydrogen bonds : angle 6.78565 / 4.72 ( 1263) link_ALPHA1-3 : bond 0.00182 / 0.09 ( 3) link_ALPHA1-3 : angle 1.78278 / 1.18 ( 9) link_ALPHA1-6 : bond 0.00050 / 0.03 ( 3) link_ALPHA1-6 : angle 1.65849 / 1.02 ( 9) link_BETA1-4 : bond 0.00352 / 0.17 ( 6) link_BETA1-4 : angle 2.26925 / 1.45 ( 18) link_NAG-ASN : bond 0.00371 / 0.21 ( 12) link_NAG-ASN : angle 1.23632 / 0.82 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.411 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 171 TYR cc_start: 0.9261 (m-80) cc_final: 0.8659 (m-80) REVERT: A 234 PHE cc_start: 0.9208 (t80) cc_final: 0.8771 (t80) REVERT: A 236 VAL cc_start: 0.8425 (t) cc_final: 0.8019 (t) REVERT: A 237 ASP cc_start: 0.9156 (t0) cc_final: 0.8787 (m-30) REVERT: J 35 ASP cc_start: 0.9446 (m-30) cc_final: 0.9132 (t70) REVERT: C 171 TYR cc_start: 0.9331 (m-80) cc_final: 0.9068 (m-80) REVERT: C 237 ASP cc_start: 0.9074 (t0) cc_final: 0.8634 (m-30) REVERT: F 548 MET cc_start: 0.7223 (mmp) cc_final: 0.6731 (mmp) REVERT: L 35 ASP cc_start: 0.9430 (m-30) cc_final: 0.9203 (m-30) REVERT: B 171 TYR cc_start: 0.9248 (m-80) cc_final: 0.8834 (m-80) REVERT: B 234 PHE cc_start: 0.9176 (t80) cc_final: 0.8968 (t80) REVERT: B 237 ASP cc_start: 0.9111 (t0) cc_final: 0.8803 (m-30) REVERT: B 273 LEU cc_start: 0.8978 (mt) cc_final: 0.8777 (mt) REVERT: E 517 TYR cc_start: 0.7315 (m-10) cc_final: 0.7085 (m-10) REVERT: E 548 MET cc_start: 0.7520 (mmp) cc_final: 0.7310 (mmt) REVERT: E 564 GLU cc_start: 0.9456 (mp0) cc_final: 0.9242 (mp0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1208 time to fit residues: 17.1483 Evaluate side-chains 62 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.032881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.026871 restraints weight = 152511.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.027859 restraints weight = 85787.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.028561 restraints weight = 56987.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.029078 restraints weight = 42248.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.029450 restraints weight = 33374.914| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13497 Z= 0.313 Angle : 0.819 10.134 18393 Z= 0.421 Chirality : 0.047 0.305 2091 Planarity : 0.005 0.043 2313 Dihedral : 6.042 26.756 1806 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.22 % Allowed : 1.65 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.28 (0.20), residues: 1626 helix: -0.59 (0.32), residues: 195 sheet: -0.27 (0.20), residues: 603 loop : 0.17 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 17 TYR 0.018 0.003 TYR B 99 PHE 0.017 0.003 PHE C 234 TRP 0.016 0.003 TRP K 36 HIS 0.007 0.002 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.31 (13464) covalent geometry : angle 0.81020 / 0.42 (18303) SS BOND : bond 0.00776 / 0.44 ( 9) SS BOND : angle 1.77013 / 1.13 ( 18) hydrogen bonds : bond 0.04924 / 3.24 ( 489) hydrogen bonds : angle 7.05064 / 4.87 ( 1263) link_ALPHA1-3 : bond 0.00043 / 0.02 ( 3) link_ALPHA1-3 : angle 2.09473 / 1.39 ( 9) link_ALPHA1-6 : bond 0.00228 / 0.11 ( 3) link_ALPHA1-6 : angle 1.96549 / 1.22 ( 9) link_BETA1-4 : bond 0.00213 / 0.09 ( 6) link_BETA1-4 : angle 1.85495 / 1.22 ( 18) link_NAG-ASN : bond 0.00307 / 0.20 ( 12) link_NAG-ASN : angle 1.92289 / 1.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.404 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: G 118 MET cc_start: 0.9065 (tmm) cc_final: 0.8699 (tmm) REVERT: A 171 TYR cc_start: 0.9368 (m-80) cc_final: 0.8762 (m-80) REVERT: A 234 PHE cc_start: 0.9092 (t80) cc_final: 0.8838 (t80) REVERT: A 237 ASP cc_start: 0.9141 (t0) cc_final: 0.8707 (m-30) REVERT: D 517 TYR cc_start: 0.7688 (m-80) cc_final: 0.7279 (m-10) REVERT: I 118 MET cc_start: 0.9149 (tmm) cc_final: 0.8919 (tmm) REVERT: C 234 PHE cc_start: 0.9153 (t80) cc_final: 0.8911 (t80) REVERT: C 237 ASP cc_start: 0.9194 (t0) cc_final: 0.8776 (m-30) REVERT: F 548 MET cc_start: 0.7764 (mmt) cc_final: 0.6625 (mmt) REVERT: H 118 MET cc_start: 0.9199 (tmm) cc_final: 0.8612 (tmm) REVERT: B 171 TYR cc_start: 0.9304 (m-80) cc_final: 0.8846 (m-80) REVERT: B 234 PHE cc_start: 0.9135 (t80) cc_final: 0.8879 (t80) REVERT: B 237 ASP cc_start: 0.9141 (t0) cc_final: 0.8677 (m-30) REVERT: E 548 MET cc_start: 0.7881 (mmt) cc_final: 0.7594 (mmt) outliers start: 3 outliers final: 0 residues processed: 87 average time/residue: 0.1109 time to fit residues: 13.9344 Evaluate side-chains 57 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 5 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 147 optimal weight: 0.0980 chunk 90 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.035026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.028996 restraints weight = 145154.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.030055 restraints weight = 80905.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.030795 restraints weight = 52986.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.031338 restraints weight = 38799.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.031721 restraints weight = 30308.606| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13497 Z= 0.117 Angle : 0.606 6.981 18393 Z= 0.315 Chirality : 0.045 0.213 2091 Planarity : 0.004 0.034 2313 Dihedral : 5.517 23.809 1806 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.17 (0.21), residues: 1626 helix: -0.35 (0.34), residues: 195 sheet: -0.34 (0.20), residues: 633 loop : 0.37 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 17 TYR 0.013 0.002 TYR C 109 PHE 0.018 0.002 PHE C 234 TRP 0.014 0.002 TRP A 275 HIS 0.005 0.001 HIS D 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (13464) covalent geometry : angle 0.59574 / 0.31 (18303) SS BOND : bond 0.00666 / 0.38 ( 9) SS BOND : angle 2.25375 / 1.34 ( 18) hydrogen bonds : bond 0.04061 / 2.65 ( 489) hydrogen bonds : angle 6.58887 / 4.60 ( 1263) link_ALPHA1-3 : bond 0.00382 / 0.19 ( 3) link_ALPHA1-3 : angle 1.53411 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00309 / 0.15 ( 3) link_ALPHA1-6 : angle 1.50637 / 0.93 ( 9) link_BETA1-4 : bond 0.00379 / 0.19 ( 6) link_BETA1-4 : angle 1.92281 / 1.26 ( 18) link_NAG-ASN : bond 0.00463 / 0.27 ( 12) link_NAG-ASN : angle 1.33319 / 0.90 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.519 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: G 118 MET cc_start: 0.8713 (tmm) cc_final: 0.8400 (tmm) REVERT: A 33 ILE cc_start: 0.8851 (tp) cc_final: 0.8642 (tp) REVERT: A 171 TYR cc_start: 0.9316 (m-80) cc_final: 0.8678 (m-80) REVERT: A 234 PHE cc_start: 0.9064 (t80) cc_final: 0.8663 (t80) REVERT: A 236 VAL cc_start: 0.8619 (t) cc_final: 0.8268 (t) REVERT: A 237 ASP cc_start: 0.9213 (t0) cc_final: 0.8822 (m-30) REVERT: A 273 LEU cc_start: 0.8804 (mt) cc_final: 0.8592 (mt) REVERT: J 35 ASP cc_start: 0.9515 (m-30) cc_final: 0.9255 (t70) REVERT: I 118 MET cc_start: 0.8920 (tmm) cc_final: 0.8629 (tmm) REVERT: C 33 ILE cc_start: 0.8751 (tp) cc_final: 0.7834 (tp) REVERT: C 234 PHE cc_start: 0.9165 (t80) cc_final: 0.8879 (t80) REVERT: F 548 MET cc_start: 0.7610 (mmt) cc_final: 0.6637 (mmp) REVERT: L 35 ASP cc_start: 0.9441 (m-30) cc_final: 0.9096 (t0) REVERT: L 53 ASP cc_start: 0.9105 (p0) cc_final: 0.8480 (m-30) REVERT: H 118 MET cc_start: 0.8903 (tmm) cc_final: 0.8676 (tmm) REVERT: B 171 TYR cc_start: 0.9266 (m-80) cc_final: 0.8780 (m-80) REVERT: B 237 ASP cc_start: 0.9154 (t0) cc_final: 0.8599 (m-30) REVERT: E 517 TYR cc_start: 0.7785 (m-80) cc_final: 0.7297 (m-80) REVERT: E 548 MET cc_start: 0.7819 (mmt) cc_final: 0.6878 (mmt) REVERT: K 35 ASP cc_start: 0.9401 (m-30) cc_final: 0.9057 (t0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1177 time to fit residues: 16.5925 Evaluate side-chains 63 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 164 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 48 optimal weight: 0.0050 chunk 153 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.034207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.028173 restraints weight = 148441.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.029215 restraints weight = 82113.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.029930 restraints weight = 53938.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.030468 restraints weight = 39687.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.030834 restraints weight = 31139.199| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13497 Z= 0.166 Angle : 0.623 8.342 18393 Z= 0.322 Chirality : 0.044 0.275 2091 Planarity : 0.004 0.037 2313 Dihedral : 5.398 23.936 1806 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.20 (0.21), residues: 1626 helix: -0.19 (0.35), residues: 195 sheet: -0.33 (0.20), residues: 633 loop : 0.26 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.012 0.002 TYR D 517 PHE 0.019 0.002 PHE C 234 TRP 0.014 0.002 TRP A 275 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (13464) covalent geometry : angle 0.61360 / 0.32 (18303) SS BOND : bond 0.00550 / 0.30 ( 9) SS BOND : angle 2.00661 / 1.28 ( 18) hydrogen bonds : bond 0.04054 / 2.65 ( 489) hydrogen bonds : angle 6.57643 / 4.61 ( 1263) link_ALPHA1-3 : bond 0.00234 / 0.12 ( 3) link_ALPHA1-3 : angle 1.70375 / 1.12 ( 9) link_ALPHA1-6 : bond 0.00070 / 0.03 ( 3) link_ALPHA1-6 : angle 1.64745 / 1.02 ( 9) link_BETA1-4 : bond 0.00280 / 0.13 ( 6) link_BETA1-4 : angle 1.79980 / 1.18 ( 18) link_NAG-ASN : bond 0.00291 / 0.16 ( 12) link_NAG-ASN : angle 1.43837 / 0.98 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.505 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: G 118 MET cc_start: 0.8698 (tmm) cc_final: 0.8366 (tmm) REVERT: A 161 LEU cc_start: 0.9510 (mt) cc_final: 0.9229 (mt) REVERT: A 171 TYR cc_start: 0.9365 (m-80) cc_final: 0.8736 (m-80) REVERT: A 234 PHE cc_start: 0.9132 (t80) cc_final: 0.8741 (t80) REVERT: A 237 ASP cc_start: 0.9296 (t0) cc_final: 0.8840 (m-30) REVERT: J 35 ASP cc_start: 0.9461 (m-30) cc_final: 0.9192 (t0) REVERT: I 118 MET cc_start: 0.8854 (tmm) cc_final: 0.8600 (tmm) REVERT: C 161 LEU cc_start: 0.9487 (mt) cc_final: 0.9232 (mt) REVERT: C 234 PHE cc_start: 0.9205 (t80) cc_final: 0.8943 (t80) REVERT: F 548 MET cc_start: 0.7666 (mmt) cc_final: 0.6400 (mmt) REVERT: L 35 ASP cc_start: 0.9505 (m-30) cc_final: 0.9303 (m-30) REVERT: H 118 MET cc_start: 0.8854 (tmm) cc_final: 0.8609 (tmm) REVERT: B 171 TYR cc_start: 0.9304 (m-80) cc_final: 0.8898 (m-80) REVERT: B 234 PHE cc_start: 0.9126 (t80) cc_final: 0.8798 (t80) REVERT: B 237 ASP cc_start: 0.9185 (t0) cc_final: 0.8668 (m-30) REVERT: E 517 TYR cc_start: 0.7899 (m-80) cc_final: 0.7354 (m-80) REVERT: E 548 MET cc_start: 0.7940 (mmt) cc_final: 0.6936 (mmt) REVERT: K 35 ASP cc_start: 0.9377 (m-30) cc_final: 0.8984 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1199 time to fit residues: 15.0848 Evaluate side-chains 57 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 87 optimal weight: 0.0770 overall best weight: 3.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.033628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.027442 restraints weight = 146872.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.028469 restraints weight = 82792.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.029204 restraints weight = 55050.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.029728 restraints weight = 40583.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.030107 restraints weight = 32161.754| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13497 Z= 0.160 Angle : 0.609 7.641 18393 Z= 0.315 Chirality : 0.044 0.237 2091 Planarity : 0.004 0.038 2313 Dihedral : 5.293 23.241 1806 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.14 (0.21), residues: 1626 helix: -0.13 (0.36), residues: 195 sheet: -0.29 (0.20), residues: 627 loop : 0.30 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 266 TYR 0.017 0.002 TYR B 99 PHE 0.018 0.002 PHE C 234 TRP 0.015 0.002 TRP A 275 HIS 0.003 0.001 HIS D 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (13464) covalent geometry : angle 0.59928 / 0.31 (18303) SS BOND : bond 0.00442 / 0.25 ( 9) SS BOND : angle 2.05017 / 1.26 ( 18) hydrogen bonds : bond 0.04013 / 2.63 ( 489) hydrogen bonds : angle 6.48671 / 4.55 ( 1263) link_ALPHA1-3 : bond 0.00263 / 0.13 ( 3) link_ALPHA1-3 : angle 1.65271 / 1.08 ( 9) link_ALPHA1-6 : bond 0.00094 / 0.05 ( 3) link_ALPHA1-6 : angle 1.61046 / 1.00 ( 9) link_BETA1-4 : bond 0.00349 / 0.17 ( 6) link_BETA1-4 : angle 1.71169 / 1.12 ( 18) link_NAG-ASN : bond 0.00251 / 0.14 ( 12) link_NAG-ASN : angle 1.49751 / 1.05 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.327 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: G 118 MET cc_start: 0.8512 (tmm) cc_final: 0.8136 (tmm) REVERT: A 161 LEU cc_start: 0.9575 (mt) cc_final: 0.9326 (mt) REVERT: A 171 TYR cc_start: 0.9365 (m-80) cc_final: 0.8746 (m-80) REVERT: A 237 ASP cc_start: 0.9291 (t0) cc_final: 0.8801 (m-30) REVERT: J 35 ASP cc_start: 0.9518 (m-30) cc_final: 0.9221 (t70) REVERT: I 118 MET cc_start: 0.8820 (tmm) cc_final: 0.8596 (tmm) REVERT: C 161 LEU cc_start: 0.9469 (mt) cc_final: 0.9216 (mt) REVERT: C 171 TYR cc_start: 0.9319 (m-80) cc_final: 0.9056 (m-80) REVERT: C 234 PHE cc_start: 0.9283 (t80) cc_final: 0.9067 (t80) REVERT: F 517 TYR cc_start: 0.7370 (m-10) cc_final: 0.7119 (m-10) REVERT: F 548 MET cc_start: 0.7735 (mmt) cc_final: 0.7285 (mmt) REVERT: L 35 ASP cc_start: 0.9499 (m-30) cc_final: 0.9089 (t0) REVERT: H 118 MET cc_start: 0.8711 (tmm) cc_final: 0.8495 (tmm) REVERT: B 171 TYR cc_start: 0.9348 (m-80) cc_final: 0.9047 (m-80) REVERT: B 234 PHE cc_start: 0.9197 (t80) cc_final: 0.8898 (t80) REVERT: B 237 ASP cc_start: 0.9136 (t0) cc_final: 0.8684 (m-30) REVERT: E 517 TYR cc_start: 0.8015 (m-80) cc_final: 0.7597 (m-10) REVERT: K 35 ASP cc_start: 0.9395 (m-30) cc_final: 0.9055 (t0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1186 time to fit residues: 14.5573 Evaluate side-chains 58 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 93 optimal weight: 0.0170 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.033446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.027289 restraints weight = 150551.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.028316 restraints weight = 84642.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.029018 restraints weight = 56318.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.029546 restraints weight = 41861.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.029927 restraints weight = 33178.190| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13497 Z= 0.171 Angle : 0.630 8.195 18393 Z= 0.325 Chirality : 0.045 0.250 2091 Planarity : 0.004 0.049 2313 Dihedral : 5.281 27.156 1806 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.21 (0.21), residues: 1626 helix: -0.15 (0.37), residues: 180 sheet: -0.35 (0.20), residues: 627 loop : 0.24 (0.24), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 26 TYR 0.012 0.002 TYR F 517 PHE 0.018 0.002 PHE C 234 TRP 0.015 0.002 TRP A 275 HIS 0.006 0.001 HIS E 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (13464) covalent geometry : angle 0.62002 / 0.32 (18303) SS BOND : bond 0.00412 / 0.22 ( 9) SS BOND : angle 2.25039 / 1.37 ( 18) hydrogen bonds : bond 0.04055 / 2.67 ( 489) hydrogen bonds : angle 6.52269 / 4.56 ( 1263) link_ALPHA1-3 : bond 0.00279 / 0.14 ( 3) link_ALPHA1-3 : angle 1.69262 / 1.11 ( 9) link_ALPHA1-6 : bond 0.00059 / 0.03 ( 3) link_ALPHA1-6 : angle 1.64775 / 1.03 ( 9) link_BETA1-4 : bond 0.00231 / 0.10 ( 6) link_BETA1-4 : angle 1.63654 / 1.07 ( 18) link_NAG-ASN : bond 0.00309 / 0.20 ( 12) link_NAG-ASN : angle 1.48616 / 1.04 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.324 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: G 118 MET cc_start: 0.8492 (tmm) cc_final: 0.8089 (tmm) REVERT: A 161 LEU cc_start: 0.9581 (mt) cc_final: 0.9347 (mt) REVERT: A 171 TYR cc_start: 0.9385 (m-80) cc_final: 0.8762 (m-80) REVERT: A 234 PHE cc_start: 0.9173 (t80) cc_final: 0.8827 (t80) REVERT: A 237 ASP cc_start: 0.9321 (t0) cc_final: 0.8990 (m-30) REVERT: J 35 ASP cc_start: 0.9510 (m-30) cc_final: 0.9249 (t0) REVERT: I 118 MET cc_start: 0.8837 (tmm) cc_final: 0.8601 (tmm) REVERT: C 161 LEU cc_start: 0.9410 (mt) cc_final: 0.9160 (mt) REVERT: C 171 TYR cc_start: 0.9357 (m-80) cc_final: 0.9088 (m-80) REVERT: F 517 TYR cc_start: 0.7159 (m-10) cc_final: 0.6877 (m-10) REVERT: F 548 MET cc_start: 0.7732 (mmt) cc_final: 0.7255 (mmt) REVERT: L 35 ASP cc_start: 0.9503 (m-30) cc_final: 0.9097 (t70) REVERT: H 118 MET cc_start: 0.8756 (tmm) cc_final: 0.8554 (tmm) REVERT: B 171 TYR cc_start: 0.9339 (m-80) cc_final: 0.9027 (m-80) REVERT: B 234 PHE cc_start: 0.9186 (t80) cc_final: 0.8865 (t80) REVERT: B 237 ASP cc_start: 0.9107 (t0) cc_final: 0.8662 (m-30) REVERT: E 517 TYR cc_start: 0.7927 (m-80) cc_final: 0.7465 (m-10) REVERT: E 548 MET cc_start: 0.7817 (mpp) cc_final: 0.7476 (mpp) REVERT: K 35 ASP cc_start: 0.9341 (m-30) cc_final: 0.9005 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1128 time to fit residues: 14.1810 Evaluate side-chains 57 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 0.0980 chunk 40 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.033863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.027690 restraints weight = 148497.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.028711 restraints weight = 82701.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.029454 restraints weight = 55037.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.029991 restraints weight = 40370.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.030388 restraints weight = 31693.696| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13497 Z= 0.141 Angle : 0.599 8.644 18393 Z= 0.309 Chirality : 0.044 0.238 2091 Planarity : 0.004 0.041 2313 Dihedral : 5.137 22.759 1806 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.16 (0.22), residues: 1626 helix: -0.08 (0.37), residues: 180 sheet: -0.33 (0.20), residues: 627 loop : 0.26 (0.24), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 26 TYR 0.016 0.001 TYR F 517 PHE 0.013 0.002 PHE H 80 TRP 0.015 0.002 TRP C 275 HIS 0.003 0.001 HIS E 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (13464) covalent geometry : angle 0.58884 / 0.31 (18303) SS BOND : bond 0.00468 / 0.26 ( 9) SS BOND : angle 2.04789 / 1.26 ( 18) hydrogen bonds : bond 0.03904 / 2.57 ( 489) hydrogen bonds : angle 6.38194 / 4.48 ( 1263) link_ALPHA1-3 : bond 0.00333 / 0.17 ( 3) link_ALPHA1-3 : angle 1.60282 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00160 / 0.08 ( 3) link_ALPHA1-6 : angle 1.56851 / 0.98 ( 9) link_BETA1-4 : bond 0.00286 / 0.14 ( 6) link_BETA1-4 : angle 1.62013 / 1.06 ( 18) link_NAG-ASN : bond 0.00304 / 0.18 ( 12) link_NAG-ASN : angle 1.43710 / 1.00 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8451 (tmm) cc_final: 0.8058 (tmm) REVERT: A 171 TYR cc_start: 0.9397 (m-80) cc_final: 0.8784 (m-80) REVERT: A 234 PHE cc_start: 0.9131 (t80) cc_final: 0.8806 (t80) REVERT: A 237 ASP cc_start: 0.9477 (t0) cc_final: 0.8954 (m-30) REVERT: J 35 ASP cc_start: 0.9508 (m-30) cc_final: 0.9246 (t0) REVERT: I 118 MET cc_start: 0.8818 (tmm) cc_final: 0.8602 (tmm) REVERT: C 161 LEU cc_start: 0.9489 (mt) cc_final: 0.9265 (mt) REVERT: C 171 TYR cc_start: 0.9308 (m-80) cc_final: 0.8950 (m-80) REVERT: C 234 PHE cc_start: 0.9204 (t80) cc_final: 0.8993 (t80) REVERT: F 517 TYR cc_start: 0.7137 (m-10) cc_final: 0.6856 (m-10) REVERT: F 548 MET cc_start: 0.7673 (mmt) cc_final: 0.7184 (mmt) REVERT: L 35 ASP cc_start: 0.9433 (m-30) cc_final: 0.9081 (t0) REVERT: B 171 TYR cc_start: 0.9342 (m-80) cc_final: 0.9028 (m-80) REVERT: B 234 PHE cc_start: 0.9171 (t80) cc_final: 0.8872 (t80) REVERT: B 237 ASP cc_start: 0.9081 (t0) cc_final: 0.8818 (m-30) REVERT: K 35 ASP cc_start: 0.9417 (m-30) cc_final: 0.9089 (t0) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1058 time to fit residues: 14.1951 Evaluate side-chains 63 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.033498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.027474 restraints weight = 156139.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.028469 restraints weight = 86881.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.029192 restraints weight = 57978.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.029694 restraints weight = 42617.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.030086 restraints weight = 33877.248| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13497 Z= 0.187 Angle : 0.647 8.276 18393 Z= 0.332 Chirality : 0.045 0.263 2091 Planarity : 0.004 0.047 2313 Dihedral : 5.212 25.857 1806 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.34 (0.21), residues: 1626 helix: -0.46 (0.36), residues: 195 sheet: -0.39 (0.20), residues: 606 loop : 0.16 (0.24), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 266 TYR 0.016 0.002 TYR B 99 PHE 0.011 0.002 PHE A 160 TRP 0.017 0.002 TRP A 275 HIS 0.010 0.001 HIS E 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (13464) covalent geometry : angle 0.63720 / 0.33 (18303) SS BOND : bond 0.00515 / 0.28 ( 9) SS BOND : angle 2.00374 / 1.24 ( 18) hydrogen bonds : bond 0.04095 / 2.71 ( 489) hydrogen bonds : angle 6.51067 / 4.56 ( 1263) link_ALPHA1-3 : bond 0.00253 / 0.13 ( 3) link_ALPHA1-3 : angle 1.73427 / 1.13 ( 9) link_ALPHA1-6 : bond 0.00051 / 0.03 ( 3) link_ALPHA1-6 : angle 1.68062 / 1.05 ( 9) link_BETA1-4 : bond 0.00225 / 0.10 ( 6) link_BETA1-4 : angle 1.54443 / 1.02 ( 18) link_NAG-ASN : bond 0.00365 / 0.24 ( 12) link_NAG-ASN : angle 1.68447 / 1.16 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.22 seconds wall clock time: 28 minutes 47.15 seconds (1727.15 seconds total)