Starting phenix.real_space_refine on Fri Jul 3 08:31:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tj5_25916/07_2026/7tj5_25916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj5_25916/07_2026/7tj5_25916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tj5_25916/07_2026/7tj5_25916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj5_25916/07_2026/7tj5_25916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tj5_25916/07_2026/7tj5_25916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj5_25916/07_2026/7tj5_25916.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tj5_25916/07_2026/7tj5_25916.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tj5_25916/07_2026/7tj5_25916.cif" } resolution = 2.41 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= 0.001 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8732 2.51 5 N 2088 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "B" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "C" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "D" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 2} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 2.79, per 1000 atoms: 0.21 Number of scatterers: 13152 At special positions: 0 Unit cell: (103.5, 103.5, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2296 8.00 N 2088 7.00 C 8732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.86 Conformation dependent library (CDL) restraints added in 544.4 milliseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 64.3% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 10 through 36 removed outlier: 4.376A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 63 removed outlier: 4.216A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.509A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.608A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 123 removed outlier: 4.075A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 removed outlier: 3.642A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 298 removed outlier: 6.557A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.625A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.527A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'B' and resid 11 through 36 removed outlier: 3.622A pdb=" N TRP B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 63 removed outlier: 4.216A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.509A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.607A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 123 removed outlier: 4.075A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 removed outlier: 3.642A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 280 through 298 removed outlier: 6.557A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.625A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.527A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 415 Processing helix chain 'C' and resid 11 through 36 removed outlier: 3.623A pdb=" N TRP C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 63 removed outlier: 4.216A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.509A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.607A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 removed outlier: 4.075A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 removed outlier: 3.642A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 280 through 298 removed outlier: 6.557A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.624A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 removed outlier: 3.527A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 415 Processing helix chain 'D' and resid 11 through 36 removed outlier: 3.622A pdb=" N TRP D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 63 removed outlier: 4.216A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.509A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.607A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 123 removed outlier: 4.074A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 removed outlier: 3.642A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 280 through 298 removed outlier: 6.557A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.625A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 removed outlier: 3.527A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 7.158A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 329 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 320 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.157A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 329 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 7.159A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 329 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.158A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 329 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1980 1.31 - 1.44: 3468 1.44 - 1.56: 7852 1.56 - 1.69: 72 1.69 - 1.81: 48 Bond restraints: 13420 Sorted by residual: bond pdb=" C LYS A 303 " pdb=" N GLY A 304 " ideal model delta sigma weight residual 1.331 1.244 0.087 1.40e-02 5.10e+03 3.88e+01 bond pdb=" C LYS D 303 " pdb=" N GLY D 304 " ideal model delta sigma weight residual 1.331 1.244 0.087 1.40e-02 5.10e+03 3.87e+01 bond pdb=" C LYS B 303 " pdb=" N GLY B 304 " ideal model delta sigma weight residual 1.331 1.244 0.087 1.40e-02 5.10e+03 3.87e+01 bond pdb=" C LYS C 303 " pdb=" N GLY C 304 " ideal model delta sigma weight residual 1.331 1.245 0.087 1.40e-02 5.10e+03 3.84e+01 bond pdb=" C PHE B 302 " pdb=" N LYS B 303 " ideal model delta sigma weight residual 1.331 1.251 0.079 1.31e-02 5.83e+03 3.65e+01 ... (remaining 13415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.99: 18007 5.99 - 11.98: 73 11.98 - 17.97: 0 17.97 - 23.96: 0 23.96 - 29.95: 44 Bond angle restraints: 18124 Sorted by residual: angle pdb=" C40 D21 A 508 " pdb=" C41 D21 A 508 " pdb=" C42 D21 A 508 " ideal model delta sigma weight residual 124.91 154.86 -29.95 3.00e+00 1.11e-01 9.97e+01 angle pdb=" C40 D21 C 602 " pdb=" C41 D21 C 602 " pdb=" C42 D21 C 602 " ideal model delta sigma weight residual 124.91 154.83 -29.92 3.00e+00 1.11e-01 9.95e+01 angle pdb=" C40 D21 B 602 " pdb=" C41 D21 B 602 " pdb=" C42 D21 B 602 " ideal model delta sigma weight residual 124.91 154.83 -29.92 3.00e+00 1.11e-01 9.95e+01 angle pdb=" C40 D21 D 602 " pdb=" C41 D21 D 602 " pdb=" C42 D21 D 602 " ideal model delta sigma weight residual 124.91 154.80 -29.89 3.00e+00 1.11e-01 9.93e+01 angle pdb=" C40 D21 D 606 " pdb=" C41 D21 D 606 " pdb=" C42 D21 D 606 " ideal model delta sigma weight residual 124.91 154.54 -29.63 3.00e+00 1.11e-01 9.75e+01 ... (remaining 18119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.86: 7680 31.86 - 63.73: 464 63.73 - 95.59: 60 95.59 - 127.46: 16 127.46 - 159.32: 32 Dihedral angle restraints: 8252 sinusoidal: 3640 harmonic: 4612 Sorted by residual: dihedral pdb=" C5' CMP C 603 " pdb=" O5' CMP C 603 " pdb=" P CMP C 603 " pdb=" O1P CMP C 603 " ideal model delta sinusoidal sigma weight residual 60.00 173.99 -113.99 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 173.99 -113.99 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" C5' CMP B 603 " pdb=" O5' CMP B 603 " pdb=" P CMP B 603 " pdb=" O1P CMP B 603 " ideal model delta sinusoidal sigma weight residual 60.00 173.99 -113.99 1 2.00e+01 2.50e-03 3.38e+01 ... (remaining 8249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1903 0.089 - 0.177: 172 0.177 - 0.266: 5 0.266 - 0.354: 4 0.354 - 0.443: 16 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CB ILE D 58 " pdb=" CA ILE D 58 " pdb=" CG1 ILE D 58 " pdb=" CG2 ILE D 58 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 2097 not shown) Planarity restraints: 2204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 116 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ILE D 116 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE D 116 " -0.019 2.00e-02 2.50e+03 pdb=" N SER D 117 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 116 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.97e+00 pdb=" C ILE A 116 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 116 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 117 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 116 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C ILE C 116 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE C 116 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 117 " -0.017 2.00e-02 2.50e+03 ... (remaining 2201 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3231 2.81 - 3.33: 11961 3.33 - 3.85: 21441 3.85 - 4.38: 24597 4.38 - 4.90: 42873 Nonbonded interactions: 104103 Sorted by model distance: nonbonded pdb=" CD2 TYR B 327 " pdb=" NE ARG B 330 " model vdw 2.285 3.420 nonbonded pdb=" CD2 TYR C 327 " pdb=" NE ARG C 330 " model vdw 2.286 3.420 nonbonded pdb=" CD2 TYR D 327 " pdb=" NE ARG D 330 " model vdw 2.286 3.420 nonbonded pdb=" CD2 TYR A 327 " pdb=" NE ARG A 330 " model vdw 2.286 3.420 nonbonded pdb=" O TYR D 262 " pdb=" OG1 THR D 266 " model vdw 2.299 3.040 ... (remaining 104098 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' and (resid 10 through 415 or (resid 505 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 506 and (name C34 or name C35 or name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C \ 44)) or (resid 507 and (name C15 or name C16 or name C19 or name C20 or name C21 \ or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name O17 or name O18 or name O22 or \ name O30 or name O32)) or (resid 508 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 o \ r name C44)))) selection = (chain 'B' and (resid 10 through 415 or (resid 605 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 606 and (name C34 or name C35 or name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C \ 44)) or (resid 607 and (name C15 or name C16 or name C19 or name C20 or name C21 \ or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name O17 or name O18 or name O22 or \ name O30 or name O32)) or (resid 608 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 o \ r name C44)))) selection = (chain 'C' and (resid 10 through 415 or (resid 605 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 606 and (name C34 or name C35 or name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C \ 44)) or (resid 607 and (name C15 or name C16 or name C19 or name C20 or name C21 \ or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name O17 or name O18 or name O22 or \ name O30 or name O32)) or (resid 608 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 o \ r name C44)))) selection = (chain 'D' and (resid 10 through 415 or (resid 605 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 606 and (name C34 or name C35 or name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C \ 44)) or (resid 607 and (name C15 or name C16 or name C19 or name C20 or name C21 \ or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name O17 or name O18 or name O22 or \ name O30 or name O32)) or (resid 608 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 o \ r name C44)))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.170 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 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 : 0.008 0.100 13420 Z= 0.445 Angle : 1.788 29.948 18124 Z= 0.714 Chirality : 0.060 0.443 2100 Planarity : 0.008 0.075 2204 Dihedral : 22.998 159.320 5276 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.22 % Allowed : 19.12 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1552 helix: 1.08 (0.16), residues: 1016 sheet: -1.15 (0.45), residues: 124 loop : -0.97 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 384 TYR 0.016 0.002 TYR A 404 PHE 0.016 0.001 PHE A 365 TRP 0.023 0.002 TRP C 264 HIS 0.004 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00829 / 0.45 (13420) covalent geometry : angle 1.78816 / 0.71 (18124) hydrogen bonds : bond 0.11036 / 7.62 ( 764) hydrogen bonds : angle 4.97212 / 3.65 ( 2232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.354 Fit side-chains outliers start: 3 outliers final: 4 residues processed: 141 average time/residue: 0.8901 time to fit residues: 132.4693 Evaluate side-chains 65 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain D residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0010 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.109402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071543 restraints weight = 27735.952| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.53 r_work: 0.2946 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13420 Z= 0.158 Angle : 0.664 12.083 18124 Z= 0.323 Chirality : 0.043 0.317 2100 Planarity : 0.006 0.058 2204 Dihedral : 21.533 159.511 2324 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.38 % Allowed : 21.88 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.22), residues: 1552 helix: 2.01 (0.17), residues: 1004 sheet: -0.88 (0.47), residues: 124 loop : -0.59 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 273 TYR 0.010 0.001 TYR D 11 PHE 0.006 0.001 PHE D 309 TRP 0.010 0.001 TRP A 264 HIS 0.004 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (13420) covalent geometry : angle 0.66449 / 0.32 (18124) hydrogen bonds : bond 0.04163 / 2.72 ( 764) hydrogen bonds : angle 3.86917 / 2.85 ( 2232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LYS cc_start: 0.9043 (mttp) cc_final: 0.8636 (mttp) REVERT: A 369 MET cc_start: 0.7513 (mpp) cc_final: 0.7305 (mpp) REVERT: B 156 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8922 (mtm) REVERT: B 224 LYS cc_start: 0.8587 (pptt) cc_final: 0.8250 (mttp) REVERT: C 104 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9056 (tp) REVERT: C 277 LYS cc_start: 0.9058 (mttp) cc_final: 0.8670 (mttp) REVERT: D 277 LYS cc_start: 0.9060 (mttp) cc_final: 0.8659 (mttp) outliers start: 32 outliers final: 4 residues processed: 95 average time/residue: 0.6309 time to fit residues: 65.1013 Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN B 364 GLN C 364 GLN D 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.109354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.072008 restraints weight = 28668.211| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.56 r_work: 0.2973 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13420 Z= 0.119 Angle : 0.587 7.367 18124 Z= 0.288 Chirality : 0.042 0.299 2100 Planarity : 0.005 0.050 2204 Dihedral : 19.225 154.079 2316 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.68 % Allowed : 22.62 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.22), residues: 1552 helix: 2.24 (0.17), residues: 1000 sheet: -0.70 (0.48), residues: 124 loop : -0.32 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 391 TYR 0.008 0.001 TYR C 170 PHE 0.010 0.001 PHE C 366 TRP 0.007 0.001 TRP C 264 HIS 0.004 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13420) covalent geometry : angle 0.58657 / 0.29 (18124) hydrogen bonds : bond 0.03506 / 2.28 ( 764) hydrogen bonds : angle 3.64901 / 2.69 ( 2232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LYS cc_start: 0.9033 (mttp) cc_final: 0.8601 (mttp) REVERT: A 369 MET cc_start: 0.7653 (mpp) cc_final: 0.7409 (mpp) REVERT: B 369 MET cc_start: 0.8553 (mmm) cc_final: 0.8245 (tmm) REVERT: C 104 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9027 (tp) REVERT: C 277 LYS cc_start: 0.9055 (mttp) cc_final: 0.8652 (mttp) REVERT: C 318 GLU cc_start: 0.8923 (tt0) cc_final: 0.8590 (tt0) REVERT: C 369 MET cc_start: 0.8015 (mpp) cc_final: 0.7753 (mpp) REVERT: D 277 LYS cc_start: 0.9070 (mttp) cc_final: 0.8641 (mtmp) REVERT: D 354 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8886 (mmmt) REVERT: D 369 MET cc_start: 0.7718 (mpp) cc_final: 0.7487 (pmm) outliers start: 36 outliers final: 4 residues processed: 109 average time/residue: 0.5954 time to fit residues: 70.3050 Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 0.0770 chunk 90 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.107834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069502 restraints weight = 27896.752| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.52 r_work: 0.2891 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13420 Z= 0.182 Angle : 0.667 9.377 18124 Z= 0.318 Chirality : 0.044 0.294 2100 Planarity : 0.005 0.047 2204 Dihedral : 18.985 151.506 2316 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.08 % Allowed : 22.47 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.22), residues: 1552 helix: 2.26 (0.17), residues: 1000 sheet: -0.69 (0.53), residues: 92 loop : -0.05 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 391 TYR 0.012 0.001 TYR B 170 PHE 0.006 0.001 PHE D 366 TRP 0.008 0.001 TRP C 264 HIS 0.005 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (13420) covalent geometry : angle 0.66743 / 0.32 (18124) hydrogen bonds : bond 0.04187 / 2.74 ( 764) hydrogen bonds : angle 3.66869 / 2.70 ( 2232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LYS cc_start: 0.9080 (mttp) cc_final: 0.8634 (mttp) REVERT: A 289 MET cc_start: 0.8679 (tpp) cc_final: 0.8469 (mmm) REVERT: A 318 GLU cc_start: 0.8832 (tt0) cc_final: 0.8612 (tt0) REVERT: A 369 MET cc_start: 0.7444 (mpp) cc_final: 0.7172 (mpp) REVERT: B 394 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8615 (tptp) REVERT: C 104 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9089 (tp) REVERT: C 318 GLU cc_start: 0.8911 (tt0) cc_final: 0.8535 (tt0) REVERT: C 369 MET cc_start: 0.7832 (mpp) cc_final: 0.7398 (mpp) REVERT: D 277 LYS cc_start: 0.9087 (mttp) cc_final: 0.8637 (mtmp) REVERT: D 318 GLU cc_start: 0.8824 (tt0) cc_final: 0.8580 (tt0) REVERT: D 369 MET cc_start: 0.7461 (mpp) cc_final: 0.7247 (mpp) outliers start: 28 outliers final: 9 residues processed: 103 average time/residue: 0.6800 time to fit residues: 75.7779 Evaluate side-chains 83 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.108721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071605 restraints weight = 27871.467| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.47 r_work: 0.2934 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13420 Z= 0.123 Angle : 0.616 8.969 18124 Z= 0.296 Chirality : 0.042 0.278 2100 Planarity : 0.004 0.045 2204 Dihedral : 18.325 147.833 2316 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.41 % Allowed : 22.62 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.22), residues: 1552 helix: 2.31 (0.17), residues: 1000 sheet: -0.68 (0.46), residues: 124 loop : 0.06 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 391 TYR 0.013 0.001 TYR B 11 PHE 0.007 0.001 PHE D 366 TRP 0.006 0.001 TRP C 264 HIS 0.005 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (13420) covalent geometry : angle 0.61614 / 0.30 (18124) hydrogen bonds : bond 0.03539 / 2.29 ( 764) hydrogen bonds : angle 3.54533 / 2.61 ( 2232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8554 (tpp) cc_final: 0.8337 (mmm) REVERT: A 318 GLU cc_start: 0.8799 (tt0) cc_final: 0.8470 (tt0) REVERT: A 334 MET cc_start: 0.8397 (ttt) cc_final: 0.8106 (tpp) REVERT: A 369 MET cc_start: 0.7466 (mpp) cc_final: 0.7201 (mpp) REVERT: B 318 GLU cc_start: 0.8808 (tt0) cc_final: 0.8590 (tt0) REVERT: B 394 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8629 (tptp) REVERT: C 104 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9090 (tp) REVERT: C 318 GLU cc_start: 0.8887 (tt0) cc_final: 0.8530 (tt0) REVERT: C 369 MET cc_start: 0.7846 (mpp) cc_final: 0.7361 (mpp) REVERT: D 277 LYS cc_start: 0.9078 (mttp) cc_final: 0.8653 (mttp) REVERT: D 318 GLU cc_start: 0.8781 (tt0) cc_final: 0.8556 (tt0) REVERT: D 334 MET cc_start: 0.8385 (ttt) cc_final: 0.8074 (tpp) REVERT: D 369 MET cc_start: 0.7546 (mpp) cc_final: 0.7307 (mpp) outliers start: 19 outliers final: 7 residues processed: 97 average time/residue: 0.6956 time to fit residues: 72.8010 Evaluate side-chains 82 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 6.9990 chunk 81 optimal weight: 0.0570 chunk 118 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.107312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.069778 restraints weight = 27550.440| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.44 r_work: 0.2900 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13420 Z= 0.162 Angle : 0.656 12.374 18124 Z= 0.313 Chirality : 0.044 0.289 2100 Planarity : 0.004 0.044 2204 Dihedral : 18.271 147.132 2316 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.26 % Allowed : 22.77 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.23), residues: 1552 helix: 2.15 (0.17), residues: 1024 sheet: -0.61 (0.52), residues: 92 loop : 0.17 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 111 TYR 0.011 0.001 TYR C 170 PHE 0.009 0.001 PHE D 365 TRP 0.007 0.001 TRP C 264 HIS 0.005 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (13420) covalent geometry : angle 0.65629 / 0.31 (18124) hydrogen bonds : bond 0.03977 / 2.59 ( 764) hydrogen bonds : angle 3.56181 / 2.62 ( 2232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8626 (tpp) cc_final: 0.8406 (mmm) REVERT: A 334 MET cc_start: 0.8338 (ttt) cc_final: 0.8052 (tpp) REVERT: A 369 MET cc_start: 0.7412 (mpp) cc_final: 0.7161 (mpp) REVERT: B 277 LYS cc_start: 0.9200 (mttp) cc_final: 0.8827 (mttp) REVERT: B 318 GLU cc_start: 0.8790 (tt0) cc_final: 0.8474 (tt0) REVERT: B 394 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8619 (tptp) REVERT: C 91 LEU cc_start: 0.9497 (tp) cc_final: 0.9259 (tt) REVERT: C 104 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9109 (tp) REVERT: C 274 GLU cc_start: 0.8793 (mp0) cc_final: 0.8273 (mp0) REVERT: C 318 GLU cc_start: 0.8896 (tt0) cc_final: 0.8526 (tt0) REVERT: C 334 MET cc_start: 0.8366 (ttt) cc_final: 0.8010 (tpp) REVERT: C 369 MET cc_start: 0.7850 (mpp) cc_final: 0.7376 (mpp) REVERT: D 277 LYS cc_start: 0.9101 (mttp) cc_final: 0.8659 (mttp) REVERT: D 318 GLU cc_start: 0.8796 (tt0) cc_final: 0.8595 (tt0) REVERT: D 334 MET cc_start: 0.8317 (ttt) cc_final: 0.8022 (tpp) REVERT: D 369 MET cc_start: 0.7469 (mpp) cc_final: 0.7201 (mpp) outliers start: 17 outliers final: 7 residues processed: 92 average time/residue: 0.7767 time to fit residues: 76.9313 Evaluate side-chains 79 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.108603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071122 restraints weight = 27223.934| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.41 r_work: 0.2920 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13420 Z= 0.127 Angle : 0.639 15.566 18124 Z= 0.303 Chirality : 0.043 0.287 2100 Planarity : 0.004 0.043 2204 Dihedral : 17.892 148.082 2316 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.97 % Allowed : 23.59 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.22), residues: 1552 helix: 2.33 (0.17), residues: 1000 sheet: -0.62 (0.46), residues: 124 loop : 0.27 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.013 0.001 TYR D 11 PHE 0.006 0.001 PHE A 366 TRP 0.006 0.001 TRP C 264 HIS 0.005 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13420) covalent geometry : angle 0.63856 / 0.30 (18124) hydrogen bonds : bond 0.03545 / 2.29 ( 764) hydrogen bonds : angle 3.49478 / 2.57 ( 2232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8603 (tpp) cc_final: 0.8365 (mmm) REVERT: A 334 MET cc_start: 0.8349 (ttt) cc_final: 0.8071 (tpp) REVERT: A 369 MET cc_start: 0.7482 (mpp) cc_final: 0.7230 (mpp) REVERT: B 274 GLU cc_start: 0.8750 (mp0) cc_final: 0.8267 (mp0) REVERT: B 277 LYS cc_start: 0.9173 (mttp) cc_final: 0.8775 (mttp) REVERT: B 394 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8764 (tptt) REVERT: C 91 LEU cc_start: 0.9479 (tp) cc_final: 0.9230 (tt) REVERT: C 104 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9096 (tp) REVERT: C 274 GLU cc_start: 0.8781 (mp0) cc_final: 0.8262 (mp0) REVERT: C 318 GLU cc_start: 0.8843 (tt0) cc_final: 0.8470 (tt0) REVERT: C 334 MET cc_start: 0.8383 (ttt) cc_final: 0.8050 (tpp) REVERT: C 369 MET cc_start: 0.7887 (mpp) cc_final: 0.7375 (mpp) REVERT: D 274 GLU cc_start: 0.8739 (mp0) cc_final: 0.8258 (mp0) REVERT: D 318 GLU cc_start: 0.8757 (tt0) cc_final: 0.8547 (tt0) REVERT: D 334 MET cc_start: 0.8293 (ttt) cc_final: 0.8010 (tpp) REVERT: D 369 MET cc_start: 0.7426 (mpp) cc_final: 0.7160 (mpp) outliers start: 13 outliers final: 6 residues processed: 92 average time/residue: 0.7745 time to fit residues: 76.7545 Evaluate side-chains 80 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 139 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.108683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.071560 restraints weight = 27420.087| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.40 r_work: 0.2993 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13420 Z= 0.144 Angle : 0.673 17.324 18124 Z= 0.315 Chirality : 0.043 0.292 2100 Planarity : 0.004 0.042 2204 Dihedral : 17.650 147.362 2316 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.49 % Allowed : 23.29 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.23), residues: 1552 helix: 2.15 (0.17), residues: 1028 sheet: -0.64 (0.47), residues: 124 loop : 0.42 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 391 TYR 0.012 0.001 TYR C 11 PHE 0.006 0.001 PHE B 365 TRP 0.006 0.001 TRP C 264 HIS 0.005 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (13420) covalent geometry : angle 0.67309 / 0.32 (18124) hydrogen bonds : bond 0.03729 / 2.41 ( 764) hydrogen bonds : angle 3.48254 / 2.55 ( 2232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8765 (mp0) cc_final: 0.8290 (mp0) REVERT: A 289 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8428 (mmm) REVERT: A 334 MET cc_start: 0.8323 (ttt) cc_final: 0.8051 (tpp) REVERT: A 369 MET cc_start: 0.7430 (mpp) cc_final: 0.7144 (mpp) REVERT: B 274 GLU cc_start: 0.8798 (mp0) cc_final: 0.8272 (mp0) REVERT: B 277 LYS cc_start: 0.9186 (mttp) cc_final: 0.8789 (mttp) REVERT: B 369 MET cc_start: 0.8609 (mmm) cc_final: 0.8100 (tmm) REVERT: B 394 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8674 (tptp) REVERT: C 91 LEU cc_start: 0.9476 (tp) cc_final: 0.9235 (tt) REVERT: C 104 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9108 (tp) REVERT: C 274 GLU cc_start: 0.8808 (mp0) cc_final: 0.8259 (mp0) REVERT: C 318 GLU cc_start: 0.8858 (tt0) cc_final: 0.8490 (tt0) REVERT: C 334 MET cc_start: 0.8374 (ttt) cc_final: 0.8043 (tpp) REVERT: C 369 MET cc_start: 0.7892 (mpp) cc_final: 0.7423 (mpp) REVERT: D 274 GLU cc_start: 0.8752 (mp0) cc_final: 0.8251 (mp0) REVERT: D 334 MET cc_start: 0.8293 (ttt) cc_final: 0.8007 (tpp) REVERT: D 369 MET cc_start: 0.7434 (mpp) cc_final: 0.7188 (mpp) outliers start: 20 outliers final: 5 residues processed: 89 average time/residue: 0.7476 time to fit residues: 71.9030 Evaluate side-chains 80 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 141 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.107770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.070504 restraints weight = 27936.980| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.42 r_work: 0.2973 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13420 Z= 0.174 Angle : 0.697 15.737 18124 Z= 0.330 Chirality : 0.045 0.302 2100 Planarity : 0.004 0.042 2204 Dihedral : 17.442 147.233 2316 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.12 % Allowed : 23.51 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.23), residues: 1552 helix: 2.11 (0.17), residues: 1028 sheet: -0.55 (0.53), residues: 92 loop : 0.36 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.013 0.001 TYR D 11 PHE 0.006 0.001 PHE B 309 TRP 0.006 0.001 TRP C 264 HIS 0.005 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.17 (13420) covalent geometry : angle 0.69728 / 0.33 (18124) hydrogen bonds : bond 0.04017 / 2.61 ( 764) hydrogen bonds : angle 3.55735 / 2.61 ( 2232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8766 (mp0) cc_final: 0.8282 (mp0) REVERT: A 289 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8484 (mmm) REVERT: A 334 MET cc_start: 0.8274 (ttt) cc_final: 0.8029 (tpp) REVERT: A 369 MET cc_start: 0.7465 (mpp) cc_final: 0.7175 (mpp) REVERT: B 274 GLU cc_start: 0.8810 (mp0) cc_final: 0.8288 (mp0) REVERT: B 277 LYS cc_start: 0.9201 (mttp) cc_final: 0.8805 (mttp) REVERT: B 303 LYS cc_start: 0.9211 (mmmm) cc_final: 0.9001 (mmmm) REVERT: B 394 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8704 (tptp) REVERT: C 104 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9163 (tp) REVERT: C 274 GLU cc_start: 0.8806 (mp0) cc_final: 0.8277 (mp0) REVERT: C 277 LYS cc_start: 0.9017 (mttp) cc_final: 0.8716 (mttp) REVERT: C 303 LYS cc_start: 0.9261 (mmmm) cc_final: 0.9037 (mmmm) REVERT: C 318 GLU cc_start: 0.8864 (tt0) cc_final: 0.8620 (tt0) REVERT: C 334 MET cc_start: 0.8338 (ttt) cc_final: 0.8031 (tpp) REVERT: C 369 MET cc_start: 0.7913 (mpp) cc_final: 0.7433 (mpp) REVERT: D 274 GLU cc_start: 0.8776 (mp0) cc_final: 0.8262 (mp0) REVERT: D 303 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8968 (mmmm) REVERT: D 334 MET cc_start: 0.8273 (ttt) cc_final: 0.8019 (tpp) REVERT: D 369 MET cc_start: 0.7441 (mpp) cc_final: 0.7175 (mpp) outliers start: 15 outliers final: 6 residues processed: 85 average time/residue: 0.7131 time to fit residues: 65.1947 Evaluate side-chains 84 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 27 optimal weight: 0.0170 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.109014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072092 restraints weight = 27812.671| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.46 r_work: 0.2946 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13420 Z= 0.121 Angle : 0.667 16.229 18124 Z= 0.314 Chirality : 0.042 0.282 2100 Planarity : 0.004 0.041 2204 Dihedral : 16.781 148.233 2316 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.74 % Allowed : 23.88 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.23), residues: 1552 helix: 2.17 (0.17), residues: 1028 sheet: -0.66 (0.46), residues: 132 loop : 0.52 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 391 TYR 0.015 0.001 TYR D 128 PHE 0.007 0.001 PHE D 366 TRP 0.006 0.001 TRP C 264 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13420) covalent geometry : angle 0.66730 / 0.31 (18124) hydrogen bonds : bond 0.03268 / 2.11 ( 764) hydrogen bonds : angle 3.44577 / 2.51 ( 2232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8804 (mp0) cc_final: 0.8182 (mp0) REVERT: A 289 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8337 (mmm) REVERT: A 303 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8921 (mmmm) REVERT: A 334 MET cc_start: 0.8295 (ttt) cc_final: 0.7962 (tpt) REVERT: B 274 GLU cc_start: 0.8787 (mp0) cc_final: 0.8251 (mp0) REVERT: B 277 LYS cc_start: 0.9191 (mttp) cc_final: 0.8786 (mttp) REVERT: B 303 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8989 (mmmm) REVERT: B 369 MET cc_start: 0.8577 (mmm) cc_final: 0.8101 (tmm) REVERT: B 394 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8695 (tptp) REVERT: C 274 GLU cc_start: 0.8826 (mp0) cc_final: 0.8282 (mp0) REVERT: C 277 LYS cc_start: 0.8968 (mttp) cc_final: 0.8664 (mttp) REVERT: C 303 LYS cc_start: 0.9234 (mmmm) cc_final: 0.9010 (mmmm) REVERT: C 318 GLU cc_start: 0.8834 (tt0) cc_final: 0.8556 (tt0) REVERT: C 334 MET cc_start: 0.8314 (ttt) cc_final: 0.7996 (tpp) REVERT: C 369 MET cc_start: 0.7837 (mpp) cc_final: 0.7353 (mpp) REVERT: D 274 GLU cc_start: 0.8783 (mp0) cc_final: 0.8151 (mp0) REVERT: D 303 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8965 (mmmm) REVERT: D 334 MET cc_start: 0.8281 (ttt) cc_final: 0.8020 (tpp) REVERT: D 369 MET cc_start: 0.7376 (mpp) cc_final: 0.7173 (mpp) outliers start: 10 outliers final: 4 residues processed: 86 average time/residue: 0.8185 time to fit residues: 75.3218 Evaluate side-chains 81 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.107383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069953 restraints weight = 27663.122| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.45 r_work: 0.2902 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13420 Z= 0.163 Angle : 0.726 22.884 18124 Z= 0.342 Chirality : 0.044 0.296 2100 Planarity : 0.004 0.041 2204 Dihedral : 16.708 146.370 2316 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.97 % Allowed : 23.74 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.23), residues: 1552 helix: 2.12 (0.17), residues: 1032 sheet: -0.64 (0.47), residues: 124 loop : 0.46 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 273 TYR 0.014 0.001 TYR B 128 PHE 0.005 0.001 PHE C 309 TRP 0.006 0.001 TRP C 264 HIS 0.004 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (13420) covalent geometry : angle 0.72624 / 0.34 (18124) hydrogen bonds : bond 0.03881 / 2.51 ( 764) hydrogen bonds : angle 3.53897 / 2.59 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6181.82 seconds wall clock time: 105 minutes 35.24 seconds (6335.24 seconds total)