Starting phenix.real_space_refine on Sat Sep 12 09:22:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ur8_20857/09_2026/6ur8_20857.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ur8_20857/09_2026/6ur8_20857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ur8_20857/09_2026/6ur8_20857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ur8_20857/09_2026/6ur8_20857.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ur8_20857/09_2026/6ur8_20857.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ur8_20857/09_2026/6ur8_20857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ur8_20857/09_2026/6ur8_20857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ur8_20857/09_2026/6ur8_20857.map" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 9779 2.51 5 N 2357 2.21 5 O 2651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2976 Classifications: {'peptide': 362} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 343} Chain breaks: 1 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2917 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2917 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "D" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2976 Classifications: {'peptide': 362} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 343} Chain breaks: 1 Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2917 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.66, per 1000 atoms: 0.25 Number of scatterers: 14880 At special positions: 0 Unit cell: (144.414, 95.9088, 120.162, 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 93 16.00 O 2651 8.00 N 2357 7.00 C 9779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.04 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 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 563.9 milliseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3498 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 18 sheets defined 36.8% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.600A pdb=" N PHE A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 removed outlier: 4.137A pdb=" N GLU A 80 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.871A pdb=" N CYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.742A pdb=" N PHE A 239 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 267 removed outlier: 3.691A pdb=" N LEU A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 removed outlier: 3.630A pdb=" N TYR A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 564 through 593 removed outlier: 3.514A pdb=" N MET A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 593 " --> pdb=" O VAL A 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 209 through 225 removed outlier: 4.227A pdb=" N ILE B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 239 through 262 Processing helix chain 'B' and resid 270 through 298 removed outlier: 3.744A pdb=" N LYS B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 334 through 365 removed outlier: 3.847A pdb=" N PHE B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 209 through 225 removed outlier: 4.227A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 239 through 262 Processing helix chain 'C' and resid 270 through 298 removed outlier: 3.745A pdb=" N LYS C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 319 through 322 Processing helix chain 'C' and resid 334 through 365 removed outlier: 3.848A pdb=" N PHE C 365 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.600A pdb=" N PHE D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 removed outlier: 4.137A pdb=" N GLU D 80 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 224 through 231 removed outlier: 3.871A pdb=" N CYS D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 241 removed outlier: 3.743A pdb=" N PHE D 239 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 267 removed outlier: 3.691A pdb=" N LEU D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 306 removed outlier: 3.630A pdb=" N TYR D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 329 Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 565 through 593 removed outlier: 3.514A pdb=" N MET D 579 " --> pdb=" O ILE D 575 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 593 " --> pdb=" O VAL D 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 209 through 225 removed outlier: 4.227A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 239 through 262 Processing helix chain 'E' and resid 270 through 299 removed outlier: 3.744A pdb=" N LYS E 274 " --> pdb=" O PRO E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 318 Processing helix chain 'E' and resid 319 through 322 Processing helix chain 'E' and resid 334 through 365 removed outlier: 3.847A pdb=" N PHE E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 87 removed outlier: 4.488A pdb=" N GLY A 121 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 164 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 38 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 51 removed outlier: 7.724A pdb=" N ALA A 45 " --> pdb=" O TRP A 62 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TRP A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU A 47 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASN A 60 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.707A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 82 removed outlier: 3.597A pdb=" N VAL B 111 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE B 119 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 113 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 82 removed outlier: 3.597A pdb=" N VAL B 111 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE B 119 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 113 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER B 44 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN B 55 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU B 63 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR B 32 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 159 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 148 removed outlier: 3.770A pdb=" N ALA B 182 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG B 206 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE B 180 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 148 Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.596A pdb=" N VAL C 111 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 119 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 113 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.596A pdb=" N VAL C 111 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 119 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 113 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER C 44 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP C 159 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 148 removed outlier: 3.770A pdb=" N ALA C 182 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG C 206 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE C 180 " --> pdb=" O ARG C 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 141 through 148 Processing sheet with id=AB3, first strand: chain 'D' and resid 85 through 87 removed outlier: 4.487A pdb=" N GLY D 121 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 164 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 38 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 44 through 51 removed outlier: 7.723A pdb=" N ALA D 45 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU D 47 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN D 60 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.707A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.597A pdb=" N VAL E 111 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE E 119 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER E 113 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.597A pdb=" N VAL E 111 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE E 119 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER E 113 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE E 51 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER E 44 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP E 159 " --> pdb=" O VAL E 31 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 141 through 148 removed outlier: 3.770A pdb=" N ALA E 182 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG E 206 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE E 180 " --> pdb=" O ARG E 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 141 through 148 713 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2296 1.31 - 1.44: 4244 1.44 - 1.57: 8596 1.57 - 1.70: 6 1.70 - 1.82: 151 Bond restraints: 15293 Sorted by residual: bond pdb=" C05 QMR D 702 " pdb=" C06 QMR D 702 " ideal model delta sigma weight residual 1.536 1.224 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" C05 QMR A 702 " pdb=" C06 QMR A 702 " ideal model delta sigma weight residual 1.536 1.225 0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" C04 QMR A 702 " pdb=" C05 QMR A 702 " ideal model delta sigma weight residual 1.536 1.229 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C04 QMR D 702 " pdb=" C05 QMR D 702 " ideal model delta sigma weight residual 1.536 1.229 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C04 QMR D 702 " pdb=" C16 QMR D 702 " ideal model delta sigma weight residual 1.507 1.730 -0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 15288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 20450 2.58 - 5.16: 359 5.16 - 7.74: 58 7.74 - 10.32: 7 10.32 - 12.90: 10 Bond angle restraints: 20884 Sorted by residual: angle pdb=" C ASP D 564 " pdb=" N TRP D 565 " pdb=" CA TRP D 565 " ideal model delta sigma weight residual 120.29 129.37 -9.08 1.42e+00 4.96e-01 4.09e+01 angle pdb=" CB ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CD1 ILE A 222 " ideal model delta sigma weight residual 113.80 122.87 -9.07 2.10e+00 2.27e-01 1.87e+01 angle pdb=" C04 QMR D 702 " pdb=" C05 QMR D 702 " pdb=" C06 QMR D 702 " ideal model delta sigma weight residual 100.12 113.02 -12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" C04 QMR A 702 " pdb=" C05 QMR A 702 " pdb=" C06 QMR A 702 " ideal model delta sigma weight residual 100.12 113.02 -12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CA SER E 15 " pdb=" CB SER E 15 " pdb=" OG SER E 15 " ideal model delta sigma weight residual 111.10 119.66 -8.56 2.00e+00 2.50e-01 1.83e+01 ... (remaining 20879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 7966 16.97 - 33.95: 815 33.95 - 50.92: 136 50.92 - 67.89: 27 67.89 - 84.87: 2 Dihedral angle restraints: 8946 sinusoidal: 3590 harmonic: 5356 Sorted by residual: dihedral pdb=" CA MET C 324 " pdb=" C MET C 324 " pdb=" N GLN C 325 " pdb=" CA GLN C 325 " ideal model delta harmonic sigma weight residual 180.00 139.02 40.98 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA MET B 324 " pdb=" C MET B 324 " pdb=" N GLN B 325 " pdb=" CA GLN B 325 " ideal model delta harmonic sigma weight residual 180.00 139.06 40.94 0 5.00e+00 4.00e-02 6.70e+01 dihedral pdb=" CA MET E 324 " pdb=" C MET E 324 " pdb=" N GLN E 325 " pdb=" CA GLN E 325 " ideal model delta harmonic sigma weight residual 180.00 139.07 40.93 0 5.00e+00 4.00e-02 6.70e+01 ... (remaining 8943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2389 0.108 - 0.216: 55 0.216 - 0.324: 11 0.324 - 0.433: 2 0.433 - 0.541: 4 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CB THR A 273 " pdb=" CA THR A 273 " pdb=" OG1 THR A 273 " pdb=" CG2 THR A 273 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" CB THR D 273 " pdb=" CA THR D 273 " pdb=" OG1 THR D 273 " pdb=" CG2 THR D 273 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" C06 QMR D 702 " pdb=" C01 QMR D 702 " pdb=" C05 QMR D 702 " pdb=" C07 QMR D 702 " both_signs ideal model delta sigma weight residual False -3.02 -2.56 -0.47 2.00e-01 2.50e+01 5.43e+00 ... (remaining 2458 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 564 " -0.015 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASP D 564 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP D 564 " -0.022 2.00e-02 2.50e+03 pdb=" N TRP D 565 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 589 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C VAL A 589 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL A 589 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY A 590 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 589 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C VAL D 589 " 0.053 2.00e-02 2.50e+03 pdb=" O VAL D 589 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY D 590 " -0.018 2.00e-02 2.50e+03 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 119 2.56 - 3.14: 12500 3.14 - 3.73: 21146 3.73 - 4.31: 28720 4.31 - 4.90: 49310 Nonbonded interactions: 111795 Sorted by model distance: nonbonded pdb=" ND2 ASN C 97 " pdb=" O MET C 101 " model vdw 1.970 3.120 nonbonded pdb=" ND2 ASN E 97 " pdb=" O MET E 101 " model vdw 1.970 3.120 nonbonded pdb=" ND2 ASN B 97 " pdb=" O MET B 101 " model vdw 1.971 3.120 nonbonded pdb=" O MET E 324 " pdb=" OH TYR E 340 " model vdw 2.074 3.040 nonbonded pdb=" O MET B 324 " pdb=" OH TYR B 340 " model vdw 2.075 3.040 ... (remaining 111790 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.290 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.710 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.010 0.312 15300 Z= 0.499 Angle : 0.859 12.903 20898 Z= 0.443 Chirality : 0.056 0.541 2461 Planarity : 0.005 0.074 2529 Dihedral : 13.535 84.869 5427 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.18 % 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: -4.52 (0.16), residues: 1778 helix: -2.17 (0.16), residues: 621 sheet: -2.86 (0.21), residues: 444 loop : -3.73 (0.19), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 7 TYR 0.012 0.001 TYR C 340 PHE 0.010 0.001 PHE A 322 TRP 0.011 0.001 TRP B 151 HIS 0.002 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.01034 / 0.50 (15293) covalent geometry : angle 0.85853 / 0.44 (20884) SS BOND : bond 0.00646 / 0.32 ( 7) SS BOND : angle 1.30983 / 0.70 ( 14) hydrogen bonds : bond 0.12176 / 7.92 ( 665) hydrogen bonds : angle 6.06492 / 4.32 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 148 ASN cc_start: 0.8642 (t0) cc_final: 0.8441 (t0) REVERT: A 178 TRP cc_start: 0.8613 (t-100) cc_final: 0.8336 (t-100) REVERT: A 572 ILE cc_start: 0.7655 (tt) cc_final: 0.7397 (mt) REVERT: B 159 ASP cc_start: 0.7915 (t0) cc_final: 0.7587 (p0) REVERT: C 132 ILE cc_start: 0.8511 (mm) cc_final: 0.8267 (mm) REVERT: D 157 THR cc_start: 0.8663 (p) cc_final: 0.8358 (t) REVERT: D 570 MET cc_start: 0.7134 (ttm) cc_final: 0.6933 (ttt) REVERT: E 77 MET cc_start: 0.6904 (mtp) cc_final: 0.6692 (ttm) outliers start: 1 outliers final: 1 residues processed: 354 average time/residue: 0.1260 time to fit residues: 64.8211 Evaluate side-chains 203 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 589 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 312 HIS B 142 GLN B 143 ASN C 109 ASN C 215 ASN D 148 ASN E 143 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132948 restraints weight = 17427.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131870 restraints weight = 22977.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132397 restraints weight = 20952.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132697 restraints weight = 17267.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.132854 restraints weight = 16149.228| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15300 Z= 0.176 Angle : 0.743 10.274 20898 Z= 0.365 Chirality : 0.047 0.156 2461 Planarity : 0.004 0.041 2529 Dihedral : 5.157 31.005 1941 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.43 % Allowed : 11.12 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.55 (0.18), residues: 1778 helix: 0.00 (0.20), residues: 614 sheet: -1.93 (0.24), residues: 414 loop : -3.01 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 207 TYR 0.012 0.001 TYR C 340 PHE 0.019 0.002 PHE A 322 TRP 0.012 0.001 TRP E 151 HIS 0.007 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (15293) covalent geometry : angle 0.74198 / 0.36 (20884) SS BOND : bond 0.01022 / 0.48 ( 7) SS BOND : angle 1.34577 / 0.79 ( 14) hydrogen bonds : bond 0.05557 / 3.63 ( 665) hydrogen bonds : angle 4.69032 / 3.35 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 277 time to evaluate : 0.346 Fit side-chains REVERT: A 12 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7630 (tt0) REVERT: A 178 TRP cc_start: 0.8575 (t-100) cc_final: 0.8284 (t-100) REVERT: A 223 ASN cc_start: 0.8281 (m-40) cc_final: 0.8026 (t0) REVERT: A 224 LEU cc_start: 0.8909 (tt) cc_final: 0.8663 (tp) REVERT: A 231 ILE cc_start: 0.8959 (pt) cc_final: 0.8577 (mt) REVERT: B 95 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5067 (m-80) REVERT: B 159 ASP cc_start: 0.7963 (t0) cc_final: 0.7592 (p0) REVERT: B 354 VAL cc_start: 0.8588 (p) cc_final: 0.8306 (t) REVERT: C 106 PHE cc_start: 0.7514 (t80) cc_final: 0.7051 (t80) REVERT: C 132 ILE cc_start: 0.8762 (mm) cc_final: 0.8539 (mm) REVERT: D 123 VAL cc_start: 0.9256 (p) cc_final: 0.8989 (t) REVERT: D 266 ILE cc_start: 0.8316 (tt) cc_final: 0.8089 (tt) outliers start: 24 outliers final: 10 residues processed: 291 average time/residue: 0.1085 time to fit residues: 47.8272 Evaluate side-chains 216 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 596 TRP Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 5 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 170 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.147680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130559 restraints weight = 17812.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.130165 restraints weight = 26635.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.131143 restraints weight = 21783.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.131021 restraints weight = 16606.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.131143 restraints weight = 14945.775| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15300 Z= 0.131 Angle : 0.646 10.119 20898 Z= 0.317 Chirality : 0.044 0.180 2461 Planarity : 0.004 0.034 2529 Dihedral : 4.688 25.105 1940 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.72 % Allowed : 14.09 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -1.58 (0.19), residues: 1778 helix: 0.78 (0.21), residues: 623 sheet: -1.36 (0.24), residues: 426 loop : -2.50 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 310 TYR 0.013 0.001 TYR D 240 PHE 0.021 0.001 PHE C 355 TRP 0.010 0.001 TRP C 338 HIS 0.008 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (15293) covalent geometry : angle 0.64573 / 0.32 (20884) SS BOND : bond 0.00749 / 0.32 ( 7) SS BOND : angle 1.24766 / 0.72 ( 14) hydrogen bonds : bond 0.04624 / 3.02 ( 665) hydrogen bonds : angle 4.32299 / 3.09 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.526 Fit side-chains REVERT: A 17 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8735 (tmtt) REVERT: B 95 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.5404 (m-80) REVERT: B 159 ASP cc_start: 0.7965 (t0) cc_final: 0.7576 (p0) REVERT: B 354 VAL cc_start: 0.8644 (p) cc_final: 0.8415 (t) REVERT: C 106 PHE cc_start: 0.7578 (t80) cc_final: 0.7203 (t80) REVERT: C 189 GLU cc_start: 0.7878 (tp30) cc_final: 0.7627 (tm-30) REVERT: C 222 LEU cc_start: 0.8604 (tt) cc_final: 0.8254 (mt) REVERT: D 123 VAL cc_start: 0.9218 (p) cc_final: 0.9003 (t) REVERT: D 231 ILE cc_start: 0.8966 (pt) cc_final: 0.8527 (mt) REVERT: D 266 ILE cc_start: 0.8306 (tt) cc_final: 0.7993 (tt) REVERT: D 314 MET cc_start: 0.4707 (ptt) cc_final: 0.4328 (mmt) REVERT: E 9 GLU cc_start: 0.7953 (tt0) cc_final: 0.7613 (mt-10) REVERT: E 306 MET cc_start: 0.8050 (ppp) cc_final: 0.7624 (ptm) REVERT: E 324 MET cc_start: 0.5599 (tpp) cc_final: 0.5398 (tpt) outliers start: 29 outliers final: 13 residues processed: 256 average time/residue: 0.1002 time to fit residues: 40.1527 Evaluate side-chains 217 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 10 HIS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 596 TRP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 302 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 132 optimal weight: 0.0980 chunk 169 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 32 optimal weight: 0.0270 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN D 148 ASN E 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.145738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131236 restraints weight = 17704.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.129117 restraints weight = 25158.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127845 restraints weight = 17802.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128217 restraints weight = 16444.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.128411 restraints weight = 15004.038| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15300 Z= 0.125 Angle : 0.626 12.160 20898 Z= 0.306 Chirality : 0.043 0.170 2461 Planarity : 0.004 0.034 2529 Dihedral : 4.434 25.304 1940 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.32 % Allowed : 15.81 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -1.18 (0.20), residues: 1778 helix: 1.09 (0.21), residues: 618 sheet: -1.03 (0.25), residues: 424 loop : -2.29 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 94 TYR 0.009 0.001 TYR B 95 PHE 0.025 0.001 PHE C 355 TRP 0.009 0.001 TRP D 125 HIS 0.006 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15293) covalent geometry : angle 0.62489 / 0.31 (20884) SS BOND : bond 0.00619 / 0.27 ( 7) SS BOND : angle 1.37805 / 0.81 ( 14) hydrogen bonds : bond 0.04311 / 2.82 ( 665) hydrogen bonds : angle 4.12716 / 2.94 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.487 Fit side-chains REVERT: A 12 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7421 (tt0) REVERT: B 70 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8014 (mtpt) REVERT: B 95 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.5473 (m-80) REVERT: B 101 MET cc_start: 0.6140 (ppp) cc_final: 0.5873 (ppp) REVERT: B 207 ARG cc_start: 0.8795 (ttm110) cc_final: 0.8490 (ttp-110) REVERT: C 106 PHE cc_start: 0.7551 (t80) cc_final: 0.7194 (t80) REVERT: C 157 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: D 231 ILE cc_start: 0.8934 (pt) cc_final: 0.8550 (mt) REVERT: E 49 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7143 (pt0) REVERT: E 306 MET cc_start: 0.8417 (ppp) cc_final: 0.8114 (ptm) outliers start: 39 outliers final: 26 residues processed: 244 average time/residue: 0.0997 time to fit residues: 38.1690 Evaluate side-chains 220 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 596 TRP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 47 optimal weight: 0.0770 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 142 GLN E 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.144363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.124934 restraints weight = 17850.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124542 restraints weight = 17740.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.124859 restraints weight = 17170.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.125019 restraints weight = 16463.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.125220 restraints weight = 15710.035| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15300 Z= 0.120 Angle : 0.604 12.178 20898 Z= 0.295 Chirality : 0.043 0.173 2461 Planarity : 0.004 0.034 2529 Dihedral : 4.345 24.527 1940 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.79 % Allowed : 17.12 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.93 (0.20), residues: 1778 helix: 1.22 (0.21), residues: 620 sheet: -0.86 (0.25), residues: 412 loop : -2.09 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 122 TYR 0.013 0.001 TYR B 17 PHE 0.026 0.001 PHE C 355 TRP 0.008 0.001 TRP D 67 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (15293) covalent geometry : angle 0.60296 / 0.30 (20884) SS BOND : bond 0.00708 / 0.30 ( 7) SS BOND : angle 1.33963 / 0.78 ( 14) hydrogen bonds : bond 0.04235 / 2.78 ( 665) hydrogen bonds : angle 4.01474 / 2.86 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.524 Fit side-chains REVERT: A 266 ILE cc_start: 0.8005 (tt) cc_final: 0.7747 (tt) REVERT: B 70 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7748 (mtpt) REVERT: B 95 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.5587 (m-80) REVERT: B 145 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8747 (p) REVERT: C 106 PHE cc_start: 0.7653 (t80) cc_final: 0.7278 (t80) REVERT: C 157 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: C 196 TYR cc_start: 0.8379 (t80) cc_final: 0.8153 (t80) REVERT: C 364 MET cc_start: 0.4272 (OUTLIER) cc_final: 0.3808 (ttm) REVERT: E 9 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7664 (mt-10) REVERT: E 49 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7208 (pt0) REVERT: E 199 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8717 (mp) REVERT: E 222 LEU cc_start: 0.8515 (tt) cc_final: 0.8234 (tp) outliers start: 47 outliers final: 30 residues processed: 246 average time/residue: 0.0925 time to fit residues: 36.3112 Evaluate side-chains 228 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 10 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 596 TRP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 4 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.142492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.123835 restraints weight = 17851.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123556 restraints weight = 17976.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.123891 restraints weight = 16518.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123982 restraints weight = 15055.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.124067 restraints weight = 14631.304| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15300 Z= 0.124 Angle : 0.615 13.348 20898 Z= 0.302 Chirality : 0.043 0.181 2461 Planarity : 0.004 0.038 2529 Dihedral : 4.296 25.252 1940 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.15 % Allowed : 18.07 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.78 (0.20), residues: 1778 helix: 1.33 (0.21), residues: 620 sheet: -0.71 (0.25), residues: 406 loop : -2.02 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 310 TYR 0.014 0.001 TYR B 17 PHE 0.027 0.001 PHE C 355 TRP 0.011 0.001 TRP D 596 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15293) covalent geometry : angle 0.61383 / 0.30 (20884) SS BOND : bond 0.00660 / 0.29 ( 7) SS BOND : angle 1.29772 / 0.77 ( 14) hydrogen bonds : bond 0.04280 / 2.81 ( 665) hydrogen bonds : angle 3.97548 / 2.82 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.407 Fit side-chains REVERT: A 266 ILE cc_start: 0.8030 (tt) cc_final: 0.7776 (tt) REVERT: B 70 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7878 (mtpt) REVERT: B 95 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.5910 (m-80) REVERT: B 145 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8673 (p) REVERT: C 106 PHE cc_start: 0.7668 (t80) cc_final: 0.7291 (t80) REVERT: C 157 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: C 196 TYR cc_start: 0.8419 (t80) cc_final: 0.8146 (t80) REVERT: E 9 GLU cc_start: 0.8057 (tt0) cc_final: 0.7778 (mt-10) REVERT: E 49 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7239 (pt0) REVERT: E 199 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8684 (mp) REVERT: E 222 LEU cc_start: 0.8563 (tt) cc_final: 0.8340 (tp) REVERT: E 257 LEU cc_start: 0.8487 (tt) cc_final: 0.8239 (mp) REVERT: E 349 PHE cc_start: 0.8609 (m-80) cc_final: 0.8303 (m-80) outliers start: 53 outliers final: 32 residues processed: 235 average time/residue: 0.0876 time to fit residues: 33.3462 Evaluate side-chains 225 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 103 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 0.0040 chunk 159 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.141148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126303 restraints weight = 17842.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.123195 restraints weight = 28257.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.123143 restraints weight = 21702.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.123368 restraints weight = 18820.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.123353 restraints weight = 16172.072| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15300 Z= 0.129 Angle : 0.624 13.335 20898 Z= 0.307 Chirality : 0.043 0.178 2461 Planarity : 0.004 0.036 2529 Dihedral : 4.320 25.286 1940 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.91 % Allowed : 18.61 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.75 (0.20), residues: 1778 helix: 1.25 (0.21), residues: 635 sheet: -0.68 (0.25), residues: 404 loop : -1.98 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 155 TYR 0.015 0.001 TYR B 17 PHE 0.026 0.001 PHE C 355 TRP 0.011 0.001 TRP E 151 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (15293) covalent geometry : angle 0.62372 / 0.31 (20884) SS BOND : bond 0.00674 / 0.30 ( 7) SS BOND : angle 1.27011 / 0.73 ( 14) hydrogen bonds : bond 0.04417 / 2.90 ( 665) hydrogen bonds : angle 3.96290 / 2.81 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8084 (tt) cc_final: 0.7792 (tt) REVERT: B 29 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: B 95 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: B 145 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8680 (p) REVERT: C 106 PHE cc_start: 0.7737 (t80) cc_final: 0.7282 (t80) REVERT: C 157 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: E 9 GLU cc_start: 0.7962 (tt0) cc_final: 0.7663 (mt-10) REVERT: E 199 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8696 (mp) REVERT: E 257 LEU cc_start: 0.8479 (tt) cc_final: 0.8182 (mp) REVERT: E 349 PHE cc_start: 0.8624 (m-80) cc_final: 0.8268 (m-80) outliers start: 49 outliers final: 34 residues processed: 239 average time/residue: 0.0926 time to fit residues: 35.2192 Evaluate side-chains 223 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.136930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.118353 restraints weight = 18023.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.117863 restraints weight = 17826.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.118051 restraints weight = 16684.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118167 restraints weight = 15470.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118199 restraints weight = 15070.367| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15300 Z= 0.163 Angle : 0.676 13.770 20898 Z= 0.330 Chirality : 0.045 0.184 2461 Planarity : 0.004 0.036 2529 Dihedral : 4.542 25.234 1940 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.62 % Allowed : 19.14 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.77 (0.20), residues: 1778 helix: 1.30 (0.21), residues: 623 sheet: -0.75 (0.25), residues: 394 loop : -1.95 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.017 0.001 TYR B 95 PHE 0.026 0.002 PHE C 355 TRP 0.011 0.001 TRP C 151 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (15293) covalent geometry : angle 0.67549 / 0.33 (20884) SS BOND : bond 0.00660 / 0.30 ( 7) SS BOND : angle 1.24256 / 0.72 ( 14) hydrogen bonds : bond 0.05080 / 3.31 ( 665) hydrogen bonds : angle 4.14311 / 2.93 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8172 (tt) cc_final: 0.7896 (tt) REVERT: B 52 MET cc_start: 0.8510 (ttp) cc_final: 0.8198 (ptm) REVERT: B 145 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 268 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6941 (m-30) REVERT: C 106 PHE cc_start: 0.7674 (t80) cc_final: 0.7295 (t80) REVERT: C 157 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: E 9 GLU cc_start: 0.7887 (tt0) cc_final: 0.7579 (mt-10) REVERT: E 199 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8686 (mp) REVERT: E 222 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8179 (mp) REVERT: E 257 LEU cc_start: 0.8585 (tt) cc_final: 0.8252 (mp) REVERT: E 349 PHE cc_start: 0.8597 (m-80) cc_final: 0.8209 (m-80) outliers start: 44 outliers final: 34 residues processed: 239 average time/residue: 0.1018 time to fit residues: 38.1846 Evaluate side-chains 232 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 48 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 HIS ** D 223 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 = 0.3476 r_free = 0.3476 target = 0.137666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.118863 restraints weight = 17974.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.118825 restraints weight = 16041.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.119027 restraints weight = 14934.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.119097 restraints weight = 14115.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.119165 restraints weight = 13905.936| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15300 Z= 0.137 Angle : 0.655 14.079 20898 Z= 0.318 Chirality : 0.044 0.191 2461 Planarity : 0.004 0.037 2529 Dihedral : 4.480 25.436 1940 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.50 % Allowed : 20.04 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.68 (0.20), residues: 1778 helix: 1.42 (0.21), residues: 623 sheet: -0.67 (0.25), residues: 398 loop : -1.98 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 48 TYR 0.015 0.001 TYR C 196 PHE 0.025 0.001 PHE C 355 TRP 0.015 0.001 TRP E 151 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15293) covalent geometry : angle 0.65443 / 0.32 (20884) SS BOND : bond 0.00655 / 0.29 ( 7) SS BOND : angle 1.21193 / 0.70 ( 14) hydrogen bonds : bond 0.04626 / 3.02 ( 665) hydrogen bonds : angle 4.06403 / 2.87 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.561 Fit side-chains REVERT: A 266 ILE cc_start: 0.8148 (tt) cc_final: 0.7841 (tt) REVERT: B 52 MET cc_start: 0.8484 (ttp) cc_final: 0.8269 (ptm) REVERT: B 145 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8649 (p) REVERT: C 106 PHE cc_start: 0.7618 (t80) cc_final: 0.7256 (t80) REVERT: C 157 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: D 317 TRP cc_start: 0.7544 (p-90) cc_final: 0.7244 (p-90) REVERT: E 9 GLU cc_start: 0.7884 (tt0) cc_final: 0.7560 (mt-10) REVERT: E 199 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8673 (mp) REVERT: E 222 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8209 (mp) REVERT: E 257 LEU cc_start: 0.8602 (tt) cc_final: 0.8230 (mp) REVERT: E 349 PHE cc_start: 0.8564 (m-80) cc_final: 0.8132 (m-80) outliers start: 42 outliers final: 33 residues processed: 228 average time/residue: 0.0921 time to fit residues: 33.4054 Evaluate side-chains 224 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 46 optimal weight: 0.0470 chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 127 optimal weight: 0.0370 chunk 99 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** D 223 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 = 0.3504 r_free = 0.3504 target = 0.139999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120452 restraints weight = 18013.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121316 restraints weight = 15927.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.121570 restraints weight = 14183.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.121796 restraints weight = 12992.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121962 restraints weight = 13003.872| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15300 Z= 0.122 Angle : 0.638 14.364 20898 Z= 0.309 Chirality : 0.043 0.191 2461 Planarity : 0.004 0.036 2529 Dihedral : 4.338 25.547 1940 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.20 % Allowed : 20.10 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.57 (0.20), residues: 1778 helix: 1.53 (0.21), residues: 623 sheet: -0.61 (0.25), residues: 404 loop : -1.93 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 48 TYR 0.016 0.001 TYR B 95 PHE 0.024 0.001 PHE C 355 TRP 0.015 0.001 TRP E 151 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (15293) covalent geometry : angle 0.63739 / 0.31 (20884) SS BOND : bond 0.00663 / 0.29 ( 7) SS BOND : angle 1.20860 / 0.70 ( 14) hydrogen bonds : bond 0.04170 / 2.73 ( 665) hydrogen bonds : angle 3.93653 / 2.79 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8093 (tt) cc_final: 0.7799 (tt) REVERT: B 145 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8623 (p) REVERT: C 106 PHE cc_start: 0.7548 (t80) cc_final: 0.7176 (t80) REVERT: C 157 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: D 317 TRP cc_start: 0.7649 (p-90) cc_final: 0.7356 (p-90) REVERT: E 9 GLU cc_start: 0.7887 (tt0) cc_final: 0.7639 (mt-10) REVERT: E 257 LEU cc_start: 0.8522 (tt) cc_final: 0.8193 (mp) REVERT: E 349 PHE cc_start: 0.8526 (m-80) cc_final: 0.8136 (m-80) outliers start: 37 outliers final: 30 residues processed: 222 average time/residue: 0.0957 time to fit residues: 34.0808 Evaluate side-chains 214 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 97 optimal weight: 0.4980 chunk 154 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.138552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.119711 restraints weight = 17961.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119524 restraints weight = 17434.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119697 restraints weight = 16406.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.119805 restraints weight = 15181.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.119892 restraints weight = 14867.442| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15300 Z= 0.138 Angle : 0.661 14.055 20898 Z= 0.321 Chirality : 0.044 0.194 2461 Planarity : 0.004 0.035 2529 Dihedral : 4.405 25.488 1940 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.20 % Allowed : 20.69 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.59 (0.20), residues: 1778 helix: 1.48 (0.21), residues: 623 sheet: -0.59 (0.25), residues: 406 loop : -1.94 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 155 TYR 0.017 0.001 TYR B 95 PHE 0.024 0.001 PHE C 355 TRP 0.013 0.001 TRP E 151 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15293) covalent geometry : angle 0.66033 / 0.32 (20884) SS BOND : bond 0.00673 / 0.30 ( 7) SS BOND : angle 1.20180 / 0.70 ( 14) hydrogen bonds : bond 0.04485 / 2.95 ( 665) hydrogen bonds : angle 4.00921 / 2.83 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2197.33 seconds wall clock time: 38 minutes 53.42 seconds (2333.42 seconds total)