Starting phenix.real_space_refine on Sat Sep 12 02:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tj5_25916/09_2026/7tj5_25916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj5_25916/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tj5_25916/09_2026/7tj5_25916.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tj5_25916/09_2026/7tj5_25916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tj5_25916/09_2026/7tj5_25916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj5_25916/09_2026/7tj5_25916.map" model { file = "/net/cci-nas-00/data/ceres_data/7tj5_25916/09_2026/7tj5_25916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj5_25916/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 2.93, per 1000 atoms: 0.22 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: 1.00 Conformation dependent library (CDL) restraints added in 556.3 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: 0.36 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: 1.91 Time building geometry restraints manager: 1.31 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: 17991 5.99 - 11.98: 89 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: 64 95.59 - 127.46: 16 127.46 - 159.32: 28 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: 1899 0.089 - 0.177: 172 0.177 - 0.266: 9 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: 1.370 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.720 Find NCS groups from input model: 0.320 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- 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= 0.446 Angle : 1.806 29.948 18124 Z= 0.716 Chirality : 0.061 0.443 2100 Planarity : 0.008 0.075 2204 Dihedral : 22.742 159.320 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 0.00831 / 0.45 (13420) covalent geometry : angle 1.80618 / 0.72 (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 : 0.498 Fit side-chains outliers start: 3 outliers final: 4 residues processed: 141 average time/residue: 0.9621 time to fit residues: 143.3371 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 : 0.352 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071498 restraints weight = 27735.635| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.54 r_work: 0.2948 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1993 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= 0.150 Angle : 0.693 11.795 18124 Z= 0.324 Chirality : 0.044 0.312 2100 Planarity : 0.006 0.057 2204 Dihedral : 20.497 156.041 2324 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.16 % Allowed : 22.17 % Favored : 75.67 % 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: 1.49 (0.22), residues: 1552 helix: 1.84 (0.17), residues: 1028 sheet: -0.86 (0.47), residues: 124 loop : -0.56 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 273 TYR 0.010 0.001 TYR C 170 PHE 0.007 0.001 PHE C 366 TRP 0.009 0.001 TRP A 264 HIS 0.004 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (13420) covalent geometry : angle 0.69284 / 0.32 (18124) hydrogen bonds : bond 0.04179 / 2.73 ( 764) hydrogen bonds : angle 3.87871 / 2.86 ( 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 104 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LYS cc_start: 0.9053 (mttp) cc_final: 0.8644 (mttp) REVERT: A 354 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8872 (mmmt) REVERT: A 369 MET cc_start: 0.7619 (mpp) cc_final: 0.7393 (mpp) REVERT: B 156 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8915 (mtm) REVERT: B 224 LYS cc_start: 0.8584 (pptt) cc_final: 0.8249 (mttp) REVERT: B 354 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8983 (mmmt) REVERT: C 104 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9049 (tp) REVERT: C 277 LYS cc_start: 0.9064 (mttp) cc_final: 0.8672 (mttp) REVERT: D 277 LYS cc_start: 0.9091 (mttp) cc_final: 0.8713 (mttp) REVERT: D 369 MET cc_start: 0.7653 (mpp) cc_final: 0.7433 (mpp) outliers start: 29 outliers final: 4 residues processed: 92 average time/residue: 0.6898 time to fit residues: 68.4644 Evaluate side-chains 68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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: 0.4980 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.0970 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.110752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073139 restraints weight = 28615.002| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.57 r_work: 0.2978 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13420 Z= 0.111 Angle : 0.620 8.386 18124 Z= 0.287 Chirality : 0.042 0.302 2100 Planarity : 0.005 0.050 2204 Dihedral : 18.267 153.813 2316 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.75 % Allowed : 22.25 % Favored : 75.00 % 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: 1.97 (0.22), residues: 1552 helix: 2.26 (0.17), residues: 1000 sheet: -0.69 (0.48), residues: 124 loop : -0.33 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 391 TYR 0.008 0.001 TYR C 170 PHE 0.008 0.001 PHE C 366 TRP 0.007 0.001 TRP C 264 HIS 0.004 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13420) covalent geometry : angle 0.61955 / 0.29 (18124) hydrogen bonds : bond 0.03424 / 2.23 ( 764) hydrogen bonds : angle 3.64076 / 2.68 ( 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 124 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LYS cc_start: 0.8991 (mttp) cc_final: 0.8550 (mttp) REVERT: A 369 MET cc_start: 0.7627 (mpp) cc_final: 0.7356 (mpp) REVERT: B 354 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8992 (mmmm) REVERT: C 104 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9020 (tp) REVERT: C 318 GLU cc_start: 0.8925 (tt0) cc_final: 0.8592 (tt0) REVERT: C 369 MET cc_start: 0.8011 (mpp) cc_final: 0.7754 (mpp) REVERT: D 277 LYS cc_start: 0.9038 (mttp) cc_final: 0.8613 (mtmp) REVERT: D 369 MET cc_start: 0.7652 (mpp) cc_final: 0.7399 (mpp) outliers start: 37 outliers final: 4 residues processed: 112 average time/residue: 0.6774 time to fit residues: 82.1460 Evaluate side-chains 77 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 0.6980 chunk 90 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.108333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.070202 restraints weight = 27980.192| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.54 r_work: 0.2908 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2663 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= 0.152 Angle : 0.683 9.861 18124 Z= 0.312 Chirality : 0.044 0.275 2100 Planarity : 0.005 0.045 2204 Dihedral : 17.820 150.544 2316 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.16 % Allowed : 22.47 % 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: 2.04 (0.23), residues: 1552 helix: 2.14 (0.17), residues: 1024 sheet: -0.63 (0.47), residues: 124 loop : 0.04 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 136 TYR 0.011 0.001 TYR B 170 PHE 0.007 0.001 PHE C 365 TRP 0.008 0.001 TRP C 264 HIS 0.005 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (13420) covalent geometry : angle 0.68328 / 0.31 (18124) hydrogen bonds : bond 0.03997 / 2.61 ( 764) hydrogen bonds : angle 3.62653 / 2.67 ( 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: 29 poor density : 83 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LYS cc_start: 0.9072 (mttp) cc_final: 0.8629 (mttp) REVERT: A 318 GLU cc_start: 0.8848 (tt0) cc_final: 0.8510 (tt0) REVERT: A 369 MET cc_start: 0.7485 (mpp) cc_final: 0.7200 (mpp) REVERT: C 104 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9084 (tp) REVERT: C 289 MET cc_start: 0.8671 (tpp) cc_final: 0.8394 (mmm) REVERT: C 318 GLU cc_start: 0.8922 (tt0) cc_final: 0.8554 (tt0) REVERT: C 369 MET cc_start: 0.7668 (mpp) cc_final: 0.7303 (mpp) REVERT: D 277 LYS cc_start: 0.9076 (mttp) cc_final: 0.8631 (mtmp) REVERT: D 289 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8418 (mmm) REVERT: D 318 GLU cc_start: 0.8836 (tt0) cc_final: 0.8573 (tt0) REVERT: D 369 MET cc_start: 0.7592 (mpp) cc_final: 0.7310 (mpp) outliers start: 29 outliers final: 8 residues processed: 100 average time/residue: 0.7261 time to fit residues: 78.6065 Evaluate side-chains 82 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 26 TYR Chi-restraints excluded: chain B residue 139 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.108007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070782 restraints weight = 28057.511| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.46 r_work: 0.2914 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2818 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= 0.139 Angle : 0.660 11.824 18124 Z= 0.301 Chirality : 0.043 0.266 2100 Planarity : 0.004 0.044 2204 Dihedral : 17.318 145.173 2316 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.26 % Allowed : 22.92 % Favored : 75.82 % 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: 2.08 (0.23), residues: 1552 helix: 2.13 (0.17), residues: 1024 sheet: -0.64 (0.47), residues: 124 loop : 0.17 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 391 TYR 0.012 0.001 TYR B 11 PHE 0.007 0.001 PHE D 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 0.00338 / 0.14 (13420) covalent geometry : angle 0.65968 / 0.30 (18124) hydrogen bonds : bond 0.03730 / 2.42 ( 764) hydrogen bonds : angle 3.55492 / 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 101 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8554 (tpp) cc_final: 0.8344 (mmm) REVERT: A 334 MET cc_start: 0.8397 (ttt) cc_final: 0.8086 (tpp) REVERT: A 369 MET cc_start: 0.7448 (mpp) cc_final: 0.7151 (mpp) REVERT: B 277 LYS cc_start: 0.9188 (mttp) cc_final: 0.8817 (mttp) REVERT: C 104 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9089 (tp) REVERT: C 289 MET cc_start: 0.8584 (tpp) cc_final: 0.8308 (mmm) REVERT: C 318 GLU cc_start: 0.8862 (tt0) cc_final: 0.8483 (tt0) REVERT: C 369 MET cc_start: 0.7692 (mpp) cc_final: 0.7303 (mpp) REVERT: D 289 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8343 (mmm) REVERT: D 318 GLU cc_start: 0.8764 (tt0) cc_final: 0.8539 (tt0) REVERT: D 334 MET cc_start: 0.8348 (ttt) cc_final: 0.8026 (tpp) REVERT: D 369 MET cc_start: 0.7505 (mpp) cc_final: 0.7214 (mpp) outliers start: 17 outliers final: 7 residues processed: 94 average time/residue: 0.7612 time to fit residues: 77.3316 Evaluate side-chains 80 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 144 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.108767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071782 restraints weight = 27496.945| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.45 r_work: 0.2934 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13420 Z= 0.115 Angle : 0.650 14.760 18124 Z= 0.294 Chirality : 0.042 0.256 2100 Planarity : 0.004 0.043 2204 Dihedral : 16.882 144.633 2316 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.04 % Allowed : 23.59 % 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: 2.11 (0.23), residues: 1552 helix: 2.17 (0.17), residues: 1024 sheet: -0.61 (0.46), residues: 124 loop : 0.16 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 391 TYR 0.013 0.001 TYR C 11 PHE 0.007 0.001 PHE B 365 TRP 0.005 0.001 TRP C 264 HIS 0.005 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13420) covalent geometry : angle 0.64965 / 0.29 (18124) hydrogen bonds : bond 0.03378 / 2.18 ( 764) hydrogen bonds : angle 3.46591 / 2.55 ( 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 96 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 334 MET cc_start: 0.8341 (ttt) cc_final: 0.8056 (tpp) REVERT: A 369 MET cc_start: 0.7471 (mpp) cc_final: 0.7165 (mpp) REVERT: B 277 LYS cc_start: 0.9167 (mttp) cc_final: 0.8793 (mttp) REVERT: B 394 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8710 (tptt) REVERT: C 91 LEU cc_start: 0.9485 (tp) cc_final: 0.9247 (tt) REVERT: C 274 GLU cc_start: 0.8822 (mp0) cc_final: 0.8294 (mp0) REVERT: C 277 LYS cc_start: 0.9049 (mttp) cc_final: 0.8670 (mttp) REVERT: C 289 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8311 (mmm) REVERT: C 318 GLU cc_start: 0.8889 (tt0) cc_final: 0.8615 (tt0) REVERT: C 334 MET cc_start: 0.8405 (ttt) cc_final: 0.8062 (tpp) REVERT: C 369 MET cc_start: 0.7700 (mpp) cc_final: 0.7297 (mpp) REVERT: D 289 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8295 (mmm) REVERT: D 318 GLU cc_start: 0.8779 (tt0) cc_final: 0.8563 (tt0) REVERT: D 334 MET cc_start: 0.8366 (ttt) cc_final: 0.8065 (tpp) REVERT: D 369 MET cc_start: 0.7642 (mpp) cc_final: 0.7352 (mpp) outliers start: 14 outliers final: 4 residues processed: 89 average time/residue: 0.7748 time to fit residues: 74.3781 Evaluate side-chains 78 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 289 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.108341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071103 restraints weight = 27944.157| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.41 r_work: 0.2983 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3017 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= 0.156 Angle : 0.683 13.049 18124 Z= 0.313 Chirality : 0.044 0.270 2100 Planarity : 0.004 0.043 2204 Dihedral : 16.866 142.169 2316 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.11 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: 2.17 (0.17), residues: 1024 sheet: -0.63 (0.47), residues: 124 loop : 0.34 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 111 TYR 0.012 0.001 TYR D 11 PHE 0.007 0.001 PHE A 365 TRP 0.006 0.001 TRP C 264 HIS 0.005 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (13420) covalent geometry : angle 0.68263 / 0.31 (18124) hydrogen bonds : bond 0.03910 / 2.54 ( 764) hydrogen bonds : angle 3.52602 / 2.59 ( 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 95 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.8322 (ttt) cc_final: 0.8041 (tpp) REVERT: A 369 MET cc_start: 0.7474 (mpp) cc_final: 0.7148 (mpp) REVERT: B 277 LYS cc_start: 0.9182 (mttp) cc_final: 0.8791 (mttp) REVERT: B 394 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8742 (tptp) REVERT: C 91 LEU cc_start: 0.9477 (tp) cc_final: 0.9255 (tt) REVERT: C 274 GLU cc_start: 0.8789 (mp0) cc_final: 0.8239 (mp0) REVERT: C 277 LYS cc_start: 0.9053 (mttp) cc_final: 0.8678 (mttp) REVERT: C 289 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8350 (mmm) REVERT: C 318 GLU cc_start: 0.8840 (tt0) cc_final: 0.8446 (tt0) REVERT: C 334 MET cc_start: 0.8347 (ttt) cc_final: 0.8008 (tpp) REVERT: D 274 GLU cc_start: 0.8752 (mp0) cc_final: 0.8253 (mp0) REVERT: D 289 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8363 (mmm) REVERT: D 318 GLU cc_start: 0.8756 (tt0) cc_final: 0.8552 (tt0) REVERT: D 334 MET cc_start: 0.8296 (ttt) cc_final: 0.7995 (tpp) REVERT: D 369 MET cc_start: 0.7571 (mpp) cc_final: 0.7275 (mpp) outliers start: 13 outliers final: 4 residues processed: 88 average time/residue: 0.7960 time to fit residues: 75.4665 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 : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 289 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.107043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069727 restraints weight = 27400.667| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.40 r_work: 0.2963 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 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 : 0.005 0.052 13420 Z= 0.212 Angle : 0.759 19.082 18124 Z= 0.346 Chirality : 0.046 0.294 2100 Planarity : 0.004 0.042 2204 Dihedral : 16.972 142.882 2316 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.97 % Allowed : 23.88 % Favored : 75.15 % 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: 2.15 (0.23), residues: 1552 helix: 2.11 (0.17), residues: 1028 sheet: -0.54 (0.53), residues: 92 loop : 0.31 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.013 0.001 TYR C 170 PHE 0.007 0.001 PHE B 365 TRP 0.006 0.001 TRP C 264 HIS 0.005 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.21 (13420) covalent geometry : angle 0.75920 / 0.35 (18124) hydrogen bonds : bond 0.04346 / 2.83 ( 764) hydrogen bonds : angle 3.62552 / 2.67 ( 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 96 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8718 (mp0) cc_final: 0.8245 (mp0) REVERT: A 334 MET cc_start: 0.8270 (ttt) cc_final: 0.8012 (tpp) REVERT: A 369 MET cc_start: 0.7503 (mpp) cc_final: 0.7177 (mpp) REVERT: B 274 GLU cc_start: 0.8773 (mp0) cc_final: 0.8260 (mp0) REVERT: B 277 LYS cc_start: 0.9189 (mttp) cc_final: 0.8794 (mttp) REVERT: B 394 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8791 (tptt) REVERT: C 274 GLU cc_start: 0.8786 (mp0) cc_final: 0.8245 (mp0) REVERT: C 277 LYS cc_start: 0.9074 (mttp) cc_final: 0.8783 (mttp) REVERT: C 289 MET cc_start: 0.8646 (tpp) cc_final: 0.8389 (mmm) REVERT: C 318 GLU cc_start: 0.8819 (tt0) cc_final: 0.8414 (tt0) REVERT: C 334 MET cc_start: 0.8325 (ttt) cc_final: 0.7987 (tpp) REVERT: D 274 GLU cc_start: 0.8739 (mp0) cc_final: 0.8224 (mp0) REVERT: D 289 MET cc_start: 0.8637 (tpp) cc_final: 0.8390 (mmm) REVERT: D 318 GLU cc_start: 0.8747 (tt0) cc_final: 0.8543 (tt0) REVERT: D 334 MET cc_start: 0.8246 (ttt) cc_final: 0.7943 (tpp) REVERT: D 369 MET cc_start: 0.7554 (mpp) cc_final: 0.7240 (mpp) outliers start: 13 outliers final: 4 residues processed: 92 average time/residue: 0.7960 time to fit residues: 78.6404 Evaluate side-chains 78 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER 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: 0.7980 chunk 139 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 109 optimal weight: 0.0770 chunk 112 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 159 GLN D 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.110032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.073263 restraints weight = 28355.952| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.51 r_work: 0.3023 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13420 Z= 0.114 Angle : 0.675 16.515 18124 Z= 0.308 Chirality : 0.043 0.262 2100 Planarity : 0.004 0.041 2204 Dihedral : 15.984 144.679 2316 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.45 % Allowed : 24.26 % 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: 2.23 (0.23), residues: 1552 helix: 2.16 (0.17), residues: 1028 sheet: -0.65 (0.46), residues: 132 loop : 0.53 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 124 TYR 0.015 0.001 TYR B 128 PHE 0.007 0.001 PHE D 366 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 0.00264 / 0.11 (13420) covalent geometry : angle 0.67466 / 0.31 (18124) hydrogen bonds : bond 0.03173 / 2.04 ( 764) hydrogen bonds : angle 3.47940 / 2.55 ( 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 91 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.492 Fit side-chains REVERT: A 274 GLU cc_start: 0.8756 (mp0) cc_final: 0.8118 (mp0) REVERT: A 303 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8966 (mmmm) REVERT: A 334 MET cc_start: 0.8302 (ttt) cc_final: 0.8057 (tpt) REVERT: A 369 MET cc_start: 0.7643 (mpp) cc_final: 0.7317 (mpp) REVERT: B 274 GLU cc_start: 0.8762 (mp0) cc_final: 0.8227 (mp0) REVERT: B 303 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8994 (mmmm) REVERT: B 369 MET cc_start: 0.8766 (mmm) cc_final: 0.8245 (tmm) REVERT: B 394 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8863 (tptt) REVERT: C 274 GLU cc_start: 0.8820 (mp0) cc_final: 0.8269 (mp0) REVERT: C 277 LYS cc_start: 0.9096 (mttp) cc_final: 0.8783 (mttp) REVERT: C 289 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8410 (mmm) REVERT: C 303 LYS cc_start: 0.9246 (mmmm) cc_final: 0.9032 (mmmm) REVERT: C 318 GLU cc_start: 0.8859 (tt0) cc_final: 0.8489 (tt0) REVERT: C 334 MET cc_start: 0.8333 (ttt) cc_final: 0.8066 (tpp) REVERT: D 274 GLU cc_start: 0.8750 (mp0) cc_final: 0.8238 (mp0) REVERT: D 289 MET cc_start: 0.8668 (tpp) cc_final: 0.8446 (mmm) REVERT: D 303 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8964 (mmmm) REVERT: D 334 MET cc_start: 0.8309 (ttt) cc_final: 0.8056 (tpp) outliers start: 6 outliers final: 0 residues processed: 86 average time/residue: 0.8493 time to fit residues: 78.2019 Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.108501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071250 restraints weight = 27768.600| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.47 r_work: 0.2928 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13420 Z= 0.129 Angle : 0.737 23.022 18124 Z= 0.333 Chirality : 0.043 0.269 2100 Planarity : 0.004 0.041 2204 Dihedral : 15.728 141.787 2316 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.30 % Allowed : 24.33 % 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: 2.25 (0.23), residues: 1552 helix: 2.16 (0.17), residues: 1032 sheet: -0.70 (0.52), residues: 108 loop : 0.53 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 273 TYR 0.014 0.001 TYR C 11 PHE 0.006 0.001 PHE A 366 TRP 0.005 0.001 TRP C 264 HIS 0.004 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (13420) covalent geometry : angle 0.73686 / 0.33 (18124) hydrogen bonds : bond 0.03513 / 2.26 ( 764) hydrogen bonds : angle 3.53114 / 2.59 ( 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 80 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8814 (mp0) cc_final: 0.8244 (mp0) REVERT: A 303 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8974 (mmmm) REVERT: A 334 MET cc_start: 0.8256 (ttt) cc_final: 0.7933 (tpt) REVERT: B 274 GLU cc_start: 0.8797 (mp0) cc_final: 0.8214 (mp0) REVERT: B 303 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8994 (mmmm) REVERT: B 369 MET cc_start: 0.8648 (mmm) cc_final: 0.8163 (tmm) REVERT: C 274 GLU cc_start: 0.8843 (mp0) cc_final: 0.8292 (mp0) REVERT: C 277 LYS cc_start: 0.9059 (mttp) cc_final: 0.8754 (mttp) REVERT: C 289 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8374 (mmm) REVERT: C 303 LYS cc_start: 0.9236 (mmmm) cc_final: 0.9015 (mmmm) REVERT: C 318 GLU cc_start: 0.8816 (tt0) cc_final: 0.8426 (tt0) REVERT: C 334 MET cc_start: 0.8312 (ttt) cc_final: 0.8024 (tpp) REVERT: D 274 GLU cc_start: 0.8782 (mp0) cc_final: 0.8258 (mp0) REVERT: D 289 MET cc_start: 0.8598 (tpp) cc_final: 0.8371 (mmm) REVERT: D 303 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8979 (mmmm) REVERT: D 334 MET cc_start: 0.8265 (ttt) cc_final: 0.8002 (tpp) outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 0.8096 time to fit residues: 67.1829 Evaluate side-chains 79 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 156 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 45 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.109090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071418 restraints weight = 28162.904| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.54 r_work: 0.2996 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13420 Z= 0.131 Angle : 0.747 22.491 18124 Z= 0.336 Chirality : 0.044 0.271 2100 Planarity : 0.004 0.041 2204 Dihedral : 15.483 139.390 2316 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.60 % Allowed : 24.33 % Favored : 75.07 % 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: 2.14 (0.17), residues: 1032 sheet: -0.70 (0.52), residues: 108 loop : 0.51 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 273 TYR 0.015 0.001 TYR B 128 PHE 0.007 0.001 PHE D 366 TRP 0.006 0.001 TRP D 264 HIS 0.004 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (13420) covalent geometry : angle 0.74703 / 0.34 (18124) hydrogen bonds : bond 0.03520 / 2.28 ( 764) hydrogen bonds : angle 3.52749 / 2.58 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6496.42 seconds wall clock time: 111 minutes 4.86 seconds (6664.86 seconds total)