Starting phenix.real_space_refine on Wed Mar 4 16:54:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ur8_20857/03_2026/6ur8_20857.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ur8_20857/03_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_20857/03_2026/6ur8_20857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ur8_20857/03_2026/6ur8_20857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ur8_20857/03_2026/6ur8_20857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ur8_20857/03_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-dev-5986/lib/python3.9/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 dihedrals: 3 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.55, per 1000 atoms: 0.24 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: 1.32 Conformation dependent library (CDL) restraints added in 618.3 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: 0.45 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: 2.26 Time building geometry restraints manager: 1.68 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 - 19.52: 8355 19.52 - 39.05: 731 39.05 - 58.57: 82 58.57 - 78.09: 21 78.09 - 97.62: 14 Dihedral angle restraints: 9203 sinusoidal: 3847 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 9200 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: 2.220 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.010 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 14.861 97.615 5684 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 covalent geometry : bond 0.01034 (15293) covalent geometry : angle 0.85853 (20884) SS BOND : bond 0.00646 ( 7) SS BOND : angle 1.30983 ( 14) hydrogen bonds : bond 0.12176 ( 665) hydrogen bonds : angle 6.06492 ( 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 : 0.547 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: 0.1266 time to fit residues: 64.4304 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 : 0.345 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 312 HIS B 142 GLN B 143 ASN C 109 ASN C 215 ASN E 143 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.148987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133283 restraints weight = 17446.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132475 restraints weight = 22485.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.133737 restraints weight = 21464.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133593 restraints weight = 14489.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.133714 restraints weight = 12263.637| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15300 Z= 0.177 Angle : 0.737 10.243 20898 Z= 0.364 Chirality : 0.047 0.155 2461 Planarity : 0.004 0.042 2529 Dihedral : 5.780 30.431 2198 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 1.55 % Allowed : 11.18 % Favored : 87.28 % 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: -2.52 (0.18), residues: 1778 helix: 0.08 (0.20), residues: 606 sheet: -1.99 (0.23), residues: 428 loop : -2.96 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 207 TYR 0.011 0.001 TYR E 95 PHE 0.019 0.002 PHE A 322 TRP 0.012 0.001 TRP E 151 HIS 0.008 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00409 (15293) covalent geometry : angle 0.73631 (20884) SS BOND : bond 0.01082 ( 7) SS BOND : angle 1.33308 ( 14) hydrogen bonds : bond 0.05504 ( 665) hydrogen bonds : angle 4.68817 ( 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: 26 poor density : 275 time to evaluate : 0.564 Fit side-chains REVERT: A 12 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7566 (tt0) REVERT: A 178 TRP cc_start: 0.8573 (t-100) cc_final: 0.8286 (t-100) REVERT: A 223 ASN cc_start: 0.8353 (m-40) cc_final: 0.8074 (t0) REVERT: A 224 LEU cc_start: 0.8945 (tt) cc_final: 0.8610 (tp) REVERT: A 231 ILE cc_start: 0.8971 (pt) cc_final: 0.8593 (mt) REVERT: B 95 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: B 159 ASP cc_start: 0.8013 (t0) cc_final: 0.7580 (p0) REVERT: B 354 VAL cc_start: 0.8563 (p) cc_final: 0.8305 (t) REVERT: C 106 PHE cc_start: 0.7517 (t80) cc_final: 0.7068 (t80) REVERT: C 132 ILE cc_start: 0.8760 (mm) cc_final: 0.8521 (mm) REVERT: C 189 GLU cc_start: 0.7687 (tp30) cc_final: 0.7465 (tp30) REVERT: C 214 ILE cc_start: 0.8036 (mm) cc_final: 0.7603 (mm) REVERT: D 123 VAL cc_start: 0.9238 (p) cc_final: 0.8956 (t) REVERT: D 266 ILE cc_start: 0.8244 (tt) cc_final: 0.8005 (tt) REVERT: E 101 MET cc_start: 0.6491 (ppp) cc_final: 0.6259 (ppp) outliers start: 26 outliers final: 10 residues processed: 291 average time/residue: 0.1125 time to fit residues: 49.6035 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 : 0.572 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 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: 1.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.137279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.118179 restraints weight = 18178.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118021 restraints weight = 17394.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118413 restraints weight = 15552.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.118651 restraints weight = 14111.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118839 restraints weight = 13773.246| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15300 Z= 0.197 Angle : 0.738 10.895 20898 Z= 0.367 Chirality : 0.047 0.179 2461 Planarity : 0.005 0.035 2529 Dihedral : 5.326 25.257 2197 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.97 % Allowed : 14.63 % Favored : 82.40 % 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: -1.77 (0.19), residues: 1778 helix: 0.55 (0.21), residues: 623 sheet: -1.52 (0.25), residues: 402 loop : -2.47 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 122 TYR 0.019 0.002 TYR B 95 PHE 0.021 0.002 PHE C 355 TRP 0.016 0.002 TRP A 67 HIS 0.008 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00472 (15293) covalent geometry : angle 0.73696 (20884) SS BOND : bond 0.00735 ( 7) SS BOND : angle 1.35013 ( 14) hydrogen bonds : bond 0.05924 ( 665) hydrogen bonds : angle 4.68830 ( 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 290 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.607 Fit side-chains REVERT: A 90 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 145 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8930 (p) REVERT: C 106 PHE cc_start: 0.7675 (t80) cc_final: 0.7280 (t80) REVERT: C 157 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: C 222 LEU cc_start: 0.8610 (tt) cc_final: 0.8299 (mt) REVERT: D 123 VAL cc_start: 0.9216 (p) cc_final: 0.8946 (t) REVERT: D 266 ILE cc_start: 0.8483 (tt) cc_final: 0.8199 (tt) REVERT: D 314 MET cc_start: 0.4962 (ptt) cc_final: 0.4445 (mmt) REVERT: E 9 GLU cc_start: 0.8049 (tt0) cc_final: 0.7800 (mt-10) REVERT: E 257 LEU cc_start: 0.8462 (tt) cc_final: 0.8213 (mp) REVERT: E 268 ASP cc_start: 0.7595 (t0) cc_final: 0.7255 (t0) outliers start: 50 outliers final: 26 residues processed: 275 average time/residue: 0.1082 time to fit residues: 46.1517 Evaluate side-chains 230 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 296 VAL 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 583 VAL 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 229 LEU Chi-restraints excluded: chain E residue 288 VAL 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: 0.8980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 157 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN E 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120876 restraints weight = 17858.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120908 restraints weight = 15979.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121005 restraints weight = 15121.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121073 restraints weight = 14955.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121120 restraints weight = 14139.076| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15300 Z= 0.142 Angle : 0.660 12.469 20898 Z= 0.324 Chirality : 0.044 0.166 2461 Planarity : 0.004 0.037 2529 Dihedral : 4.969 25.078 2197 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.68 % Allowed : 17.84 % Favored : 79.49 % 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: -1.36 (0.20), residues: 1778 helix: 0.94 (0.21), residues: 620 sheet: -1.30 (0.25), residues: 410 loop : -2.27 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 310 TYR 0.015 0.001 TYR B 95 PHE 0.024 0.001 PHE C 355 TRP 0.015 0.001 TRP E 151 HIS 0.006 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00324 (15293) covalent geometry : angle 0.65969 (20884) SS BOND : bond 0.00700 ( 7) SS BOND : angle 1.38639 ( 14) hydrogen bonds : bond 0.05077 ( 665) hydrogen bonds : angle 4.36136 ( 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 254 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.572 Fit side-chains REVERT: A 90 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7249 (mt-10) REVERT: B 268 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6668 (m-30) REVERT: C 106 PHE cc_start: 0.7713 (t80) cc_final: 0.7283 (t80) REVERT: C 222 LEU cc_start: 0.8657 (tt) cc_final: 0.8377 (mt) REVERT: D 123 VAL cc_start: 0.9232 (p) cc_final: 0.8986 (t) REVERT: D 314 MET cc_start: 0.4778 (ptt) cc_final: 0.4443 (mmt) REVERT: E 199 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8670 (mp) REVERT: E 222 LEU cc_start: 0.8596 (tt) cc_final: 0.8272 (tp) outliers start: 45 outliers final: 31 residues processed: 244 average time/residue: 0.0971 time to fit residues: 38.1956 Evaluate side-chains 218 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 A residue 222 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 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 95 TYR Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 119 HIS 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 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: 0.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 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 = 0.3445 r_free = 0.3445 target = 0.134903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.114834 restraints weight = 18184.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.115051 restraints weight = 16577.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.115305 restraints weight = 14733.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.115304 restraints weight = 13818.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.115304 restraints weight = 13818.575| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15300 Z= 0.187 Angle : 0.700 11.841 20898 Z= 0.346 Chirality : 0.046 0.174 2461 Planarity : 0.004 0.037 2529 Dihedral : 5.062 25.421 2197 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.57 % Allowed : 19.08 % Favored : 77.35 % 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: -1.30 (0.20), residues: 1778 helix: 0.95 (0.21), residues: 620 sheet: -1.24 (0.25), residues: 410 loop : -2.22 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 310 TYR 0.019 0.001 TYR B 95 PHE 0.027 0.002 PHE C 355 TRP 0.019 0.001 TRP E 151 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00453 (15293) covalent geometry : angle 0.69951 (20884) SS BOND : bond 0.00684 ( 7) SS BOND : angle 1.37348 ( 14) hydrogen bonds : bond 0.05638 ( 665) hydrogen bonds : angle 4.41982 ( 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 270 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7208 (mt-10) REVERT: C 106 PHE cc_start: 0.7826 (t80) cc_final: 0.7386 (t80) REVERT: C 157 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: C 199 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8361 (mt) REVERT: C 222 LEU cc_start: 0.8676 (tt) cc_final: 0.8428 (mt) REVERT: D 69 ASP cc_start: 0.7821 (p0) cc_final: 0.7592 (p0) REVERT: D 123 VAL cc_start: 0.9271 (p) cc_final: 0.8980 (t) REVERT: D 314 MET cc_start: 0.4823 (ptt) cc_final: 0.4601 (mmt) REVERT: E 9 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7636 (mt-10) REVERT: E 49 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: E 199 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8683 (mp) REVERT: E 222 LEU cc_start: 0.8632 (tt) cc_final: 0.8406 (tp) REVERT: E 233 LEU cc_start: 0.8579 (tp) cc_final: 0.8287 (tp) REVERT: E 324 MET cc_start: 0.5343 (tpt) cc_final: 0.5044 (tpp) outliers start: 60 outliers final: 39 residues processed: 256 average time/residue: 0.1034 time to fit residues: 41.4728 Evaluate side-chains 235 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 59 THR 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 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 291 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 95 TYR 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 173 THR Chi-restraints excluded: chain C residue 199 ILE 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 583 VAL Chi-restraints excluded: chain E residue 49 GLU 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 151 TRP Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 4 optimal weight: 0.0570 chunk 85 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN D 312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.138352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118970 restraints weight = 17885.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.118495 restraints weight = 17322.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118742 restraints weight = 16317.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.118941 restraints weight = 15635.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119090 restraints weight = 14651.568| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5289 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= 0.131 Angle : 0.636 12.788 20898 Z= 0.312 Chirality : 0.043 0.178 2461 Planarity : 0.004 0.036 2529 Dihedral : 4.718 25.316 2197 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.73 % Allowed : 20.33 % Favored : 76.93 % 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: -1.03 (0.20), residues: 1778 helix: 1.19 (0.21), residues: 620 sheet: -1.01 (0.25), residues: 406 loop : -2.12 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 310 TYR 0.013 0.001 TYR B 95 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 covalent geometry : bond 0.00299 (15293) covalent geometry : angle 0.63468 (20884) SS BOND : bond 0.00704 ( 7) SS BOND : angle 1.39993 ( 14) hydrogen bonds : bond 0.04635 ( 665) hydrogen bonds : angle 4.17788 ( 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 257 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8140 (tt) cc_final: 0.7840 (tt) REVERT: C 106 PHE cc_start: 0.7559 (t80) cc_final: 0.7191 (t80) REVERT: C 157 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: C 199 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8333 (mt) REVERT: C 222 LEU cc_start: 0.8686 (tt) cc_final: 0.8460 (mt) REVERT: D 69 ASP cc_start: 0.7771 (p0) cc_final: 0.7529 (p0) REVERT: D 123 VAL cc_start: 0.9264 (p) cc_final: 0.8990 (t) REVERT: D 226 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7564 (tt) REVERT: E 9 GLU cc_start: 0.8045 (tt0) cc_final: 0.7652 (mt-10) REVERT: E 199 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8636 (mp) REVERT: E 233 LEU cc_start: 0.8526 (tp) cc_final: 0.8277 (tp) REVERT: E 257 LEU cc_start: 0.8494 (tt) cc_final: 0.8245 (mp) REVERT: E 324 MET cc_start: 0.5133 (tpt) cc_final: 0.4888 (tpp) outliers start: 46 outliers final: 30 residues processed: 248 average time/residue: 0.0977 time to fit residues: 39.1495 Evaluate side-chains 229 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL 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 145 THR Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 37 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 173 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 226 ILE 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 296 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 103 optimal weight: 0.8980 chunk 157 optimal weight: 0.4980 chunk 131 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.136291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117884 restraints weight = 17981.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117082 restraints weight = 28185.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.117918 restraints weight = 27397.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.118087 restraints weight = 20005.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118311 restraints weight = 18376.818| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15300 Z= 0.148 Angle : 0.657 13.431 20898 Z= 0.322 Chirality : 0.044 0.177 2461 Planarity : 0.004 0.037 2529 Dihedral : 4.725 25.690 2197 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.09 % Allowed : 21.05 % Favored : 75.86 % 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: -0.98 (0.20), residues: 1778 helix: 1.21 (0.21), residues: 620 sheet: -0.96 (0.25), residues: 406 loop : -2.11 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 155 TYR 0.016 0.001 TYR B 95 PHE 0.024 0.001 PHE C 355 TRP 0.018 0.001 TRP E 151 HIS 0.006 0.001 HIS C 10 Details of bonding type rmsd covalent geometry : bond 0.00349 (15293) covalent geometry : angle 0.65594 (20884) SS BOND : bond 0.00686 ( 7) SS BOND : angle 1.32782 ( 14) hydrogen bonds : bond 0.04896 ( 665) hydrogen bonds : angle 4.18943 ( 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 255 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8266 (tt) cc_final: 0.7974 (tt) REVERT: C 106 PHE cc_start: 0.7545 (t80) cc_final: 0.7148 (t80) REVERT: C 157 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: C 199 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8373 (mt) REVERT: C 222 LEU cc_start: 0.8764 (tt) cc_final: 0.8493 (mt) REVERT: D 69 ASP cc_start: 0.7813 (p0) cc_final: 0.7535 (p0) REVERT: D 123 VAL cc_start: 0.9276 (p) cc_final: 0.9010 (t) REVERT: D 226 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7435 (tt) REVERT: D 317 TRP cc_start: 0.7574 (p-90) cc_final: 0.7293 (p-90) REVERT: E 9 GLU cc_start: 0.8016 (tt0) cc_final: 0.7679 (mt-10) REVERT: E 199 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8647 (mp) REVERT: E 222 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8184 (mp) REVERT: E 233 LEU cc_start: 0.8555 (tp) cc_final: 0.8276 (tp) REVERT: E 257 LEU cc_start: 0.8484 (tt) cc_final: 0.8219 (mp) outliers start: 52 outliers final: 37 residues processed: 244 average time/residue: 0.0978 time to fit residues: 38.5443 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 : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL 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 B residue 42 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 151 TRP 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 173 THR Chi-restraints excluded: chain C residue 199 ILE 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 119 HIS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 226 ILE 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 151 TRP Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.136678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.120721 restraints weight = 18003.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120246 restraints weight = 23851.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120497 restraints weight = 24339.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.120781 restraints weight = 19995.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120978 restraints weight = 17506.207| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5594 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= 0.143 Angle : 0.650 13.637 20898 Z= 0.318 Chirality : 0.044 0.178 2461 Planarity : 0.004 0.037 2529 Dihedral : 4.721 27.765 2197 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.21 % Allowed : 21.17 % Favored : 75.62 % 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: -0.85 (0.20), residues: 1778 helix: 1.31 (0.21), residues: 620 sheet: -0.90 (0.25), residues: 406 loop : -2.01 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 155 TYR 0.015 0.001 TYR B 95 PHE 0.023 0.001 PHE C 355 TRP 0.016 0.001 TRP E 151 HIS 0.006 0.001 HIS C 10 Details of bonding type rmsd covalent geometry : bond 0.00334 (15293) covalent geometry : angle 0.64982 (20884) SS BOND : bond 0.00670 ( 7) SS BOND : angle 1.29558 ( 14) hydrogen bonds : bond 0.04791 ( 665) hydrogen bonds : angle 4.16696 ( 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 258 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8260 (tt) cc_final: 0.7944 (tt) REVERT: B 52 MET cc_start: 0.8562 (ttm) cc_final: 0.8252 (ptm) REVERT: C 106 PHE cc_start: 0.7461 (t80) cc_final: 0.7048 (t80) REVERT: C 157 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: C 199 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8352 (mt) REVERT: C 222 LEU cc_start: 0.8781 (tt) cc_final: 0.8489 (mt) REVERT: D 69 ASP cc_start: 0.7740 (p0) cc_final: 0.7486 (p0) REVERT: D 123 VAL cc_start: 0.9284 (p) cc_final: 0.9020 (t) REVERT: D 226 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7518 (tt) REVERT: D 317 TRP cc_start: 0.7663 (p-90) cc_final: 0.7402 (p-90) REVERT: E 9 GLU cc_start: 0.7950 (tt0) cc_final: 0.7722 (mt-10) REVERT: E 199 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8646 (mp) REVERT: E 222 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8206 (mp) REVERT: E 233 LEU cc_start: 0.8523 (tp) cc_final: 0.8282 (tp) REVERT: E 257 LEU cc_start: 0.8520 (tt) cc_final: 0.8257 (mp) outliers start: 54 outliers final: 41 residues processed: 249 average time/residue: 0.0971 time to fit residues: 38.9664 Evaluate side-chains 237 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 TRP 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 230 VAL 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 173 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 296 VAL 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 226 ILE 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 151 TRP Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 222 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.137114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120821 restraints weight = 17927.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120226 restraints weight = 26558.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121531 restraints weight = 23739.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120927 restraints weight = 14419.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120915 restraints weight = 13135.442| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5686 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= 0.137 Angle : 0.652 13.880 20898 Z= 0.318 Chirality : 0.043 0.178 2461 Planarity : 0.004 0.037 2529 Dihedral : 4.659 29.609 2197 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.91 % Allowed : 21.76 % Favored : 75.33 % 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: -0.82 (0.20), residues: 1778 helix: 1.34 (0.21), residues: 620 sheet: -0.86 (0.25), residues: 406 loop : -2.01 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 155 TYR 0.015 0.001 TYR B 95 PHE 0.022 0.001 PHE C 355 TRP 0.016 0.001 TRP E 151 HIS 0.006 0.001 HIS C 10 Details of bonding type rmsd covalent geometry : bond 0.00318 (15293) covalent geometry : angle 0.65138 (20884) SS BOND : bond 0.00676 ( 7) SS BOND : angle 1.26770 ( 14) hydrogen bonds : bond 0.04646 ( 665) hydrogen bonds : angle 4.12604 ( 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 248 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8250 (tt) cc_final: 0.7934 (tt) REVERT: B 52 MET cc_start: 0.8558 (ttm) cc_final: 0.8288 (ptm) REVERT: C 106 PHE cc_start: 0.7515 (t80) cc_final: 0.7166 (t80) REVERT: C 157 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: C 199 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8288 (mt) REVERT: C 222 LEU cc_start: 0.8715 (tt) cc_final: 0.8437 (mt) REVERT: D 69 ASP cc_start: 0.7800 (p0) cc_final: 0.7553 (p0) REVERT: D 123 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9012 (t) REVERT: D 226 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7415 (tt) REVERT: D 317 TRP cc_start: 0.7753 (p-90) cc_final: 0.7457 (p-90) REVERT: E 9 GLU cc_start: 0.7967 (tt0) cc_final: 0.7668 (mt-10) REVERT: E 49 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: E 199 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8619 (mp) REVERT: E 222 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8153 (mp) REVERT: E 233 LEU cc_start: 0.8568 (tp) cc_final: 0.8297 (tp) REVERT: E 257 LEU cc_start: 0.8457 (tt) cc_final: 0.8146 (mp) outliers start: 49 outliers final: 37 residues processed: 237 average time/residue: 0.0909 time to fit residues: 35.1843 Evaluate side-chains 237 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL 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 B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 108 SER 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 230 VAL 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 173 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 199 ILE 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 123 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 49 GLU 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 151 TRP Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 165 optimal weight: 0.2980 chunk 101 optimal weight: 0.7980 chunk 168 optimal weight: 0.0470 chunk 90 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 116 optimal weight: 0.0070 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.140232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124669 restraints weight = 17958.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.123583 restraints weight = 24334.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124226 restraints weight = 22776.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124236 restraints weight = 17985.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.124580 restraints weight = 15744.349| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5814 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= 0.115 Angle : 0.625 14.165 20898 Z= 0.304 Chirality : 0.042 0.189 2461 Planarity : 0.004 0.035 2529 Dihedral : 4.466 29.034 2197 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.08 % Allowed : 22.83 % Favored : 75.09 % 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: -0.64 (0.20), residues: 1778 helix: 1.53 (0.21), residues: 622 sheet: -0.70 (0.25), residues: 404 loop : -1.99 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 155 TYR 0.013 0.001 TYR B 95 PHE 0.021 0.001 PHE C 355 TRP 0.015 0.001 TRP E 151 HIS 0.006 0.001 HIS C 10 Details of bonding type rmsd covalent geometry : bond 0.00252 (15293) covalent geometry : angle 0.62465 (20884) SS BOND : bond 0.00669 ( 7) SS BOND : angle 1.27567 ( 14) hydrogen bonds : bond 0.04028 ( 665) hydrogen bonds : angle 3.98198 ( 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 250 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8193 (tt) cc_final: 0.7837 (tt) REVERT: B 52 MET cc_start: 0.8508 (ttm) cc_final: 0.8208 (ptm) REVERT: B 145 THR cc_start: 0.8890 (m) cc_final: 0.8626 (p) REVERT: C 106 PHE cc_start: 0.7416 (t80) cc_final: 0.7045 (t80) REVERT: C 157 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: C 222 LEU cc_start: 0.8719 (tt) cc_final: 0.8437 (mt) REVERT: D 69 ASP cc_start: 0.7728 (p0) cc_final: 0.7454 (p0) REVERT: D 123 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9034 (t) REVERT: D 226 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7452 (tt) REVERT: D 317 TRP cc_start: 0.7835 (p-90) cc_final: 0.7626 (p-90) REVERT: E 9 GLU cc_start: 0.7903 (tt0) cc_final: 0.7700 (mt-10) REVERT: E 199 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8624 (mp) REVERT: E 233 LEU cc_start: 0.8535 (tp) cc_final: 0.8288 (tp) REVERT: E 257 LEU cc_start: 0.8466 (tt) cc_final: 0.8190 (mp) outliers start: 35 outliers final: 25 residues processed: 239 average time/residue: 0.0940 time to fit residues: 36.5422 Evaluate side-chains 229 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 151 TRP 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 323 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 125 ILE 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 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 123 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 226 ILE 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 151 TRP Chi-restraints excluded: chain E residue 199 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 97 optimal weight: 0.0270 chunk 154 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123678 restraints weight = 17927.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.122540 restraints weight = 25318.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123172 restraints weight = 24439.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.123177 restraints weight = 18872.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.123519 restraints weight = 16299.284| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15300 Z= 0.128 Angle : 0.640 13.986 20898 Z= 0.311 Chirality : 0.043 0.182 2461 Planarity : 0.004 0.036 2529 Dihedral : 4.460 27.176 2197 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.14 % Allowed : 22.71 % Favored : 75.15 % 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: -0.61 (0.20), residues: 1778 helix: 1.54 (0.21), residues: 622 sheet: -0.68 (0.25), residues: 404 loop : -1.96 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 328 TYR 0.011 0.001 TYR B 95 PHE 0.021 0.001 PHE C 355 TRP 0.016 0.001 TRP E 151 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00296 (15293) covalent geometry : angle 0.63948 (20884) SS BOND : bond 0.00667 ( 7) SS BOND : angle 1.25284 ( 14) hydrogen bonds : bond 0.04260 ( 665) hydrogen bonds : angle 3.99311 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.95 seconds wall clock time: 37 minutes 14.96 seconds (2234.96 seconds total)