Starting phenix.real_space_refine on Thu Aug 6 03:49:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nwk_49884/08_2026/9nwk_49884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nwk_49884/08_2026/9nwk_49884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nwk_49884/08_2026/9nwk_49884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nwk_49884/08_2026/9nwk_49884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nwk_49884/08_2026/9nwk_49884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nwk_49884/08_2026/9nwk_49884.map" } resolution = 2.74 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 8484 2.51 5 N 2076 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12876 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3099 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "B" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3099 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "C" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3099 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "D" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3099 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 120 Unusual residues: {'6OU': 4} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 120 Unusual residues: {'6OU': 4} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 120 Unusual residues: {'6OU': 4} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 120 Unusual residues: {'6OU': 4} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 2} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.01, per 1000 atoms: 0.23 Number of scatterers: 12876 At special positions: 0 Unit cell: (96.1772, 96.9787, 115.413, 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 2280 8.00 N 2076 7.00 C 8484 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: 1.04 Conformation dependent library (CDL) restraints added in 641.0 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 69.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 11 through 36 removed outlier: 3.917A 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 61 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.903A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.909A pdb=" N LEU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.918A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 159 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 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 278 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.988A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.501A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.791A pdb=" N ILE A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 412' Processing helix chain 'B' and resid 11 through 36 removed outlier: 3.917A 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 61 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.903A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.909A pdb=" N LEU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.917A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 159 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 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 278 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.989A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 404 removed outlier: 3.501A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.792A pdb=" N ILE B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 407 through 412' Processing helix chain 'C' and resid 11 through 36 removed outlier: 3.917A 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 61 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.902A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.910A pdb=" N LEU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.918A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 159 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 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 278 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.989A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 404 removed outlier: 3.500A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.792A pdb=" N ILE C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 412' Processing helix chain 'D' and resid 11 through 36 removed outlier: 3.917A 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 61 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.902A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 removed outlier: 3.909A pdb=" N LEU D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.918A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 159 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 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 278 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.988A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 404 removed outlier: 3.501A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 removed outlier: 3.792A pdb=" N ILE D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 407 through 412' Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 7.119A pdb=" N VAL A 381 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.689A 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 322 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.118A pdb=" N VAL B 381 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.689A 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 322 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 7.119A pdb=" N VAL C 381 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 3.688A 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 322 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.119A pdb=" N VAL D 381 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2089 1.32 - 1.44: 3301 1.44 - 1.57: 7702 1.57 - 1.69: 16 1.69 - 1.81: 48 Bond restraints: 13156 Sorted by residual: bond pdb=" C21 6OU C 505 " pdb=" O22 6OU C 505 " ideal model delta sigma weight residual 1.410 1.455 -0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" C21 6OU A 505 " pdb=" O22 6OU A 505 " ideal model delta sigma weight residual 1.410 1.455 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C21 6OU D 501 " pdb=" O22 6OU D 501 " ideal model delta sigma weight residual 1.410 1.454 -0.044 2.00e-02 2.50e+03 4.92e+00 bond pdb=" C21 6OU B 505 " pdb=" O22 6OU B 505 " ideal model delta sigma weight residual 1.410 1.454 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" C21 6OU A 502 " pdb=" O22 6OU A 502 " ideal model delta sigma weight residual 1.410 1.454 -0.044 2.00e-02 2.50e+03 4.88e+00 ... (remaining 13151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 17395 2.05 - 4.10: 308 4.10 - 6.14: 81 6.14 - 8.19: 40 8.19 - 10.24: 16 Bond angle restraints: 17840 Sorted by residual: angle pdb=" CA LYS D 354 " pdb=" CB LYS D 354 " pdb=" CG LYS D 354 " ideal model delta sigma weight residual 114.10 121.82 -7.72 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CA LYS A 354 " pdb=" CB LYS A 354 " pdb=" CG LYS A 354 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CA LYS C 354 " pdb=" CB LYS C 354 " pdb=" CG LYS C 354 " ideal model delta sigma weight residual 114.10 121.78 -7.68 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CA LYS B 354 " pdb=" CB LYS B 354 " pdb=" CG LYS B 354 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" C1' CMP D 503 " pdb=" C2' CMP D 503 " pdb=" C3' CMP D 503 " ideal model delta sigma weight residual 111.00 100.76 10.24 3.00e+00 1.11e-01 1.16e+01 ... (remaining 17835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 7660 35.42 - 70.83: 240 70.83 - 106.25: 40 106.25 - 141.67: 40 141.67 - 177.08: 16 Dihedral angle restraints: 7996 sinusoidal: 3420 harmonic: 4576 Sorted by residual: dihedral pdb=" C3' CMP B 501 " pdb=" O3' CMP B 501 " pdb=" P CMP B 501 " pdb=" O1P CMP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 99.54 -159.54 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C3' CMP C 501 " pdb=" O3' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 99.53 -159.53 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C3' CMP D 503 " pdb=" O3' CMP D 503 " pdb=" P CMP D 503 " pdb=" O1P CMP D 503 " ideal model delta sinusoidal sigma weight residual -60.00 99.52 -159.52 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 7993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1714 0.053 - 0.107: 325 0.107 - 0.160: 37 0.160 - 0.213: 4 0.213 - 0.267: 4 Chirality restraints: 2084 Sorted by residual: chirality pdb=" C2' CMP D 503 " pdb=" C1' CMP D 503 " pdb=" C3' CMP D 503 " pdb=" O2' CMP D 503 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C2' CMP C 501 " pdb=" C1' CMP C 501 " pdb=" C3' CMP C 501 " pdb=" O2' CMP C 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C2' CMP A 501 " pdb=" C1' CMP A 501 " pdb=" C3' CMP A 501 " pdb=" O2' CMP A 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2081 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 58 " 0.016 5.00e-02 4.00e+02 2.48e-02 9.81e-01 pdb=" N PRO D 59 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 58 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.69e-01 pdb=" N PRO B 59 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 58 " -0.016 5.00e-02 4.00e+02 2.45e-02 9.63e-01 pdb=" N PRO C 59 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " -0.014 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 7150 3.01 - 3.48: 14127 3.48 - 3.96: 21868 3.96 - 4.43: 25384 4.43 - 4.90: 38933 Nonbonded interactions: 107462 Sorted by model distance: nonbonded pdb=" O18 6OU B 504 " pdb=" O30 6OU B 504 " model vdw 2.541 2.432 nonbonded pdb=" O18 6OU D 501 " pdb=" O30 6OU D 501 " model vdw 2.541 2.432 nonbonded pdb=" O18 6OU A 504 " pdb=" O30 6OU A 504 " model vdw 2.541 2.432 nonbonded pdb=" O18 6OU C 504 " pdb=" O30 6OU C 504 " model vdw 2.541 2.432 nonbonded pdb=" C15 6OU D 505 " pdb=" C19 6OU D 505 " model vdw 2.570 3.072 ... (remaining 107457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 412 or (resid 502 and (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 C42 or name C43 or name \ C44 or name C45 or name O22 or name O30 or name O32)) or (resid 504 and (name C \ 19 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or na \ me C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 o \ r name C43 or name O18 or name O22 or name O30 or name O32)) or (resid 505 and ( \ name C19 or name C20 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 C42 or name \ C43 or name O30 or name O32)))) selection = (chain 'B' and (resid 10 through 412 or (resid 502 and (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 C42 or name C43 or name \ C44 or name C45 or name O22 or name O30 or name O32)) or (resid 504 and (name C \ 19 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or na \ me C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 o \ r name C43 or name O18 or name O22 or name O30 or name O32)) or (resid 505 and ( \ name C19 or name C20 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 C42 or name \ C43 or name O30 or name O32)))) selection = (chain 'C' and (resid 10 through 412 or (resid 502 and (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 C42 or name C43 or name \ C44 or name C45 or name O22 or name O30 or name O32)) or (resid 504 and (name C \ 19 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or na \ me C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 o \ r name C43 or name O18 or name O22 or name O30 or name O32)) or (resid 505 and ( \ name C19 or name C20 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 C42 or name \ C43 or name O30 or name O32)))) selection = (chain 'D' and (resid 10 through 412 or resid 502 or (resid 504 and (name C19 or \ name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or nam \ e C43 or name O18 or name O22 or name O30 or name O32)) or (resid 505 and (name \ C19 or name C20 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name O30 or name O32)))) } 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: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.010 Find NCS groups from input model: 0.370 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:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 : 0.004 0.045 13156 Z= 0.202 Angle : 0.781 10.238 17840 Z= 0.344 Chirality : 0.043 0.267 2084 Planarity : 0.004 0.025 2184 Dihedral : 22.361 177.083 5044 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.65 % Allowed : 20.21 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.22), residues: 1540 helix: 1.54 (0.17), residues: 980 sheet: 0.38 (0.45), residues: 112 loop : 0.27 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 235 TYR 0.010 0.001 TYR A 26 PHE 0.006 0.001 PHE D 302 TRP 0.006 0.001 TRP D 264 HIS 0.002 0.000 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (13156) covalent geometry : angle 0.78109 / 0.34 (17840) hydrogen bonds : bond 0.14242 / 9.37 ( 796) hydrogen bonds : angle 5.74884 / 4.25 ( 2316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.481 Fit side-chains REVERT: A 114 LYS cc_start: 0.9107 (tptt) cc_final: 0.8841 (tppp) REVERT: A 204 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: A 316 HIS cc_start: 0.9332 (m90) cc_final: 0.9103 (OUTLIER) REVERT: A 334 MET cc_start: 0.7884 (tmt) cc_final: 0.7453 (tmt) REVERT: A 364 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8059 (mt0) REVERT: A 369 MET cc_start: 0.9008 (mmp) cc_final: 0.8689 (mmm) REVERT: B 204 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: B 229 LYS cc_start: 0.9014 (tppp) cc_final: 0.8533 (tmtt) REVERT: B 277 LYS cc_start: 0.8831 (ptpt) cc_final: 0.8413 (ptpp) REVERT: B 334 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6991 (tmt) REVERT: B 369 MET cc_start: 0.8765 (mmp) cc_final: 0.8305 (mpm) REVERT: C 114 LYS cc_start: 0.9299 (tptt) cc_final: 0.8816 (tppp) REVERT: C 204 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8481 (mt-10) REVERT: C 289 MET cc_start: 0.9216 (mmm) cc_final: 0.8855 (mmm) REVERT: C 364 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8130 (tp-100) REVERT: C 369 MET cc_start: 0.8591 (mmp) cc_final: 0.8167 (mpm) REVERT: D 64 PHE cc_start: 0.7228 (m-10) cc_final: 0.6548 (p90) REVERT: D 114 LYS cc_start: 0.8955 (tptt) cc_final: 0.8716 (tppp) REVERT: D 204 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: D 224 LYS cc_start: 0.9168 (mttm) cc_final: 0.8860 (ptpp) REVERT: D 316 HIS cc_start: 0.9213 (m90) cc_final: 0.8846 (m90) REVERT: D 342 ASN cc_start: 0.8798 (t0) cc_final: 0.8528 (t0) REVERT: D 364 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8226 (mt0) REVERT: D 369 MET cc_start: 0.8978 (mmp) cc_final: 0.8702 (mmm) REVERT: D 412 GLN cc_start: 0.6950 (tp-100) cc_final: 0.6739 (mm-40) outliers start: 22 outliers final: 13 residues processed: 104 average time/residue: 0.5515 time to fit residues: 62.3692 Evaluate side-chains 85 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0270 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.085633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.061707 restraints weight = 37147.410| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.21 r_work: 0.3035 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13156 Z= 0.135 Angle : 0.675 10.099 17840 Z= 0.299 Chirality : 0.043 0.168 2084 Planarity : 0.004 0.027 2184 Dihedral : 19.847 176.061 2140 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.82 % Allowed : 19.24 % Favored : 76.95 % 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: 1.64 (0.22), residues: 1540 helix: 1.52 (0.17), residues: 992 sheet: 0.69 (0.47), residues: 112 loop : 0.41 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.009 0.001 TYR A 170 PHE 0.007 0.001 PHE D 302 TRP 0.007 0.001 TRP D 176 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (13156) covalent geometry : angle 0.67454 / 0.30 (17840) hydrogen bonds : bond 0.03560 / 2.33 ( 796) hydrogen bonds : angle 4.45158 / 3.28 ( 2316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 82 time to evaluate : 0.498 Fit side-chains REVERT: A 114 LYS cc_start: 0.9030 (tptt) cc_final: 0.8793 (tppp) REVERT: A 235 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7671 (ttt-90) REVERT: A 316 HIS cc_start: 0.9412 (m90) cc_final: 0.8977 (m-70) REVERT: A 334 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7420 (tmt) REVERT: A 364 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7943 (mt0) REVERT: A 369 MET cc_start: 0.8861 (mmp) cc_final: 0.8562 (mpm) REVERT: B 229 LYS cc_start: 0.9027 (tppp) cc_final: 0.8525 (tmtt) REVERT: B 277 LYS cc_start: 0.8836 (ptpt) cc_final: 0.8408 (ptpp) REVERT: B 334 MET cc_start: 0.7703 (tmt) cc_final: 0.6981 (tmt) REVERT: B 369 MET cc_start: 0.8646 (mmp) cc_final: 0.8264 (mpm) REVERT: C 114 LYS cc_start: 0.9239 (tptt) cc_final: 0.8782 (tppp) REVERT: C 364 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8112 (tp-100) REVERT: C 369 MET cc_start: 0.8517 (mmp) cc_final: 0.8185 (mpm) REVERT: D 64 PHE cc_start: 0.7339 (m-10) cc_final: 0.6605 (p90) REVERT: D 114 LYS cc_start: 0.8894 (tptt) cc_final: 0.8653 (tppp) REVERT: D 316 HIS cc_start: 0.9339 (m90) cc_final: 0.8894 (m90) REVERT: D 342 ASN cc_start: 0.8795 (t0) cc_final: 0.8485 (t0) REVERT: D 364 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8077 (mt0) REVERT: D 412 GLN cc_start: 0.6927 (tp-100) cc_final: 0.6722 (mm-40) outliers start: 51 outliers final: 8 residues processed: 125 average time/residue: 0.4916 time to fit residues: 67.8763 Evaluate side-chains 82 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 79 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS B 292 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.084843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.060657 restraints weight = 37790.266| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.22 r_work: 0.3006 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13156 Z= 0.143 Angle : 0.688 11.330 17840 Z= 0.303 Chirality : 0.042 0.159 2084 Planarity : 0.004 0.059 2184 Dihedral : 16.927 173.666 2112 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.89 % Allowed : 18.94 % Favored : 77.17 % 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: 1.64 (0.22), residues: 1540 helix: 1.53 (0.17), residues: 996 sheet: 0.88 (0.48), residues: 112 loop : 0.30 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.009 0.001 TYR D 170 PHE 0.006 0.001 PHE A 242 TRP 0.006 0.001 TRP A 176 HIS 0.002 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (13156) covalent geometry : angle 0.68752 / 0.30 (17840) hydrogen bonds : bond 0.03599 / 2.35 ( 796) hydrogen bonds : angle 4.27373 / 3.15 ( 2316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 71 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.9100 (tptt) cc_final: 0.8762 (tppp) REVERT: A 235 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8290 (tpt-90) REVERT: A 334 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7546 (tmt) REVERT: A 364 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7996 (mt0) REVERT: A 369 MET cc_start: 0.8867 (mmp) cc_final: 0.8590 (mmm) REVERT: B 334 MET cc_start: 0.7802 (tmt) cc_final: 0.7101 (tmt) REVERT: B 364 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8197 (mt0) REVERT: B 369 MET cc_start: 0.8663 (mmp) cc_final: 0.8249 (mpm) REVERT: C 369 MET cc_start: 0.8586 (mmp) cc_final: 0.8234 (mpm) REVERT: D 64 PHE cc_start: 0.7385 (m-10) cc_final: 0.6628 (p90) REVERT: D 114 LYS cc_start: 0.9042 (tptt) cc_final: 0.8763 (tppp) REVERT: D 235 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8320 (ttp80) REVERT: D 316 HIS cc_start: 0.9411 (m90) cc_final: 0.9001 (m90) REVERT: D 364 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8205 (mt0) outliers start: 52 outliers final: 15 residues processed: 116 average time/residue: 0.5346 time to fit residues: 68.2336 Evaluate side-chains 89 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 67 optimal weight: 0.5980 chunk 146 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS B 292 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.085078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061059 restraints weight = 37706.285| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.19 r_work: 0.3018 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13156 Z= 0.129 Angle : 0.675 11.272 17840 Z= 0.298 Chirality : 0.041 0.158 2084 Planarity : 0.004 0.027 2184 Dihedral : 15.783 173.899 2112 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.87 % Allowed : 17.81 % Favored : 77.32 % 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: 1.74 (0.22), residues: 1540 helix: 1.57 (0.17), residues: 996 sheet: 1.10 (0.47), residues: 116 loop : 0.34 (0.34), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.010 0.001 TYR C 170 PHE 0.006 0.001 PHE A 302 TRP 0.005 0.001 TRP B 176 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13156) covalent geometry : angle 0.67465 / 0.30 (17840) hydrogen bonds : bond 0.03308 / 2.17 ( 796) hydrogen bonds : angle 4.15506 / 3.06 ( 2316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 75 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7963 (tt) REVERT: A 114 LYS cc_start: 0.9124 (tptt) cc_final: 0.8759 (tppp) REVERT: A 238 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8648 (ptp90) REVERT: A 334 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7390 (tmt) REVERT: A 364 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8014 (mt0) REVERT: A 369 MET cc_start: 0.8876 (mmp) cc_final: 0.8674 (mmm) REVERT: B 13 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7616 (tt) REVERT: B 229 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8513 (tmtt) REVERT: B 235 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8155 (ttt-90) REVERT: B 334 MET cc_start: 0.7848 (tmt) cc_final: 0.7133 (tmt) REVERT: B 369 MET cc_start: 0.8683 (mmp) cc_final: 0.8337 (mpm) REVERT: C 13 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7902 (tt) REVERT: C 364 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8299 (mt0) REVERT: C 369 MET cc_start: 0.8640 (mmp) cc_final: 0.8370 (mpm) REVERT: D 30 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8561 (tt) REVERT: D 64 PHE cc_start: 0.7401 (m-10) cc_final: 0.6643 (p90) REVERT: D 114 LYS cc_start: 0.9085 (tptt) cc_final: 0.8766 (tppp) REVERT: D 316 HIS cc_start: 0.9456 (m90) cc_final: 0.9084 (m90) REVERT: D 364 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8192 (mt0) outliers start: 65 outliers final: 17 residues processed: 133 average time/residue: 0.4719 time to fit residues: 69.5284 Evaluate side-chains 94 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 6 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS B 292 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.084839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.059583 restraints weight = 37843.198| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.40 r_work: 0.2939 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13156 Z= 0.127 Angle : 0.679 11.792 17840 Z= 0.299 Chirality : 0.042 0.196 2084 Planarity : 0.003 0.024 2184 Dihedral : 15.149 173.681 2112 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.52 % Allowed : 19.24 % Favored : 77.25 % 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: 1.77 (0.22), residues: 1540 helix: 1.60 (0.17), residues: 996 sheet: 1.17 (0.47), residues: 116 loop : 0.33 (0.34), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 29 TYR 0.010 0.001 TYR C 170 PHE 0.004 0.001 PHE A 242 TRP 0.007 0.001 TRP B 176 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13156) covalent geometry : angle 0.67928 / 0.30 (17840) hydrogen bonds : bond 0.03230 / 2.12 ( 796) hydrogen bonds : angle 4.09824 / 3.02 ( 2316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 74 time to evaluate : 0.488 Fit side-chains REVERT: A 13 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7900 (tt) REVERT: A 114 LYS cc_start: 0.9071 (tptt) cc_final: 0.8773 (tppp) REVERT: A 238 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8469 (ptp90) REVERT: A 334 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7472 (tmt) REVERT: A 364 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7869 (mt0) REVERT: A 369 MET cc_start: 0.8874 (mmp) cc_final: 0.8667 (mmm) REVERT: B 13 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7593 (tt) REVERT: B 229 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8303 (tmtt) REVERT: B 235 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8096 (ttt-90) REVERT: B 334 MET cc_start: 0.7898 (tmt) cc_final: 0.7176 (tmt) REVERT: B 364 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8012 (mt0) REVERT: B 369 MET cc_start: 0.8727 (mmp) cc_final: 0.8386 (mpm) REVERT: C 13 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7811 (tt) REVERT: C 114 LYS cc_start: 0.9198 (tptt) cc_final: 0.8762 (tppp) REVERT: C 364 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8113 (mt0) REVERT: C 369 MET cc_start: 0.8677 (mmp) cc_final: 0.8408 (mpm) REVERT: D 13 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8259 (tt) REVERT: D 24 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8672 (mp) REVERT: D 64 PHE cc_start: 0.7568 (m-10) cc_final: 0.6695 (p90) REVERT: D 114 LYS cc_start: 0.9003 (tptt) cc_final: 0.8699 (tppp) REVERT: D 316 HIS cc_start: 0.9479 (m90) cc_final: 0.9011 (m90) REVERT: D 364 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8000 (mt0) outliers start: 47 outliers final: 18 residues processed: 118 average time/residue: 0.5132 time to fit residues: 66.8216 Evaluate side-chains 98 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 139 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS B 292 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.084724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.059567 restraints weight = 37535.873| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.38 r_work: 0.2941 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13156 Z= 0.127 Angle : 0.684 13.089 17840 Z= 0.302 Chirality : 0.042 0.195 2084 Planarity : 0.003 0.024 2184 Dihedral : 14.655 173.571 2112 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.59 % Allowed : 19.46 % Favored : 76.95 % 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: 1.80 (0.22), residues: 1540 helix: 1.64 (0.17), residues: 996 sheet: 1.09 (0.47), residues: 116 loop : 0.33 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 235 TYR 0.010 0.001 TYR C 170 PHE 0.004 0.001 PHE C 340 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13156) covalent geometry : angle 0.68411 / 0.30 (17840) hydrogen bonds : bond 0.03183 / 2.11 ( 796) hydrogen bonds : angle 4.06652 / 3.00 ( 2316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 74 time to evaluate : 0.502 Fit side-chains REVERT: A 13 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7924 (tt) REVERT: A 114 LYS cc_start: 0.9100 (tptt) cc_final: 0.8766 (tppp) REVERT: A 334 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7462 (tmt) REVERT: A 364 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7927 (mt0) REVERT: A 369 MET cc_start: 0.8892 (mmp) cc_final: 0.8691 (mmm) REVERT: B 13 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7592 (tt) REVERT: B 229 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8299 (tmtt) REVERT: B 235 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8051 (ttt-90) REVERT: B 334 MET cc_start: 0.7905 (tmt) cc_final: 0.7148 (tmt) REVERT: B 364 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7985 (mt0) REVERT: B 369 MET cc_start: 0.8747 (mmp) cc_final: 0.8438 (mpm) REVERT: C 13 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7806 (tt) REVERT: C 278 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 364 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8100 (mt0) REVERT: C 369 MET cc_start: 0.8706 (mmp) cc_final: 0.8392 (mpm) REVERT: D 13 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8255 (tt) REVERT: D 24 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8636 (mp) REVERT: D 64 PHE cc_start: 0.7572 (m-10) cc_final: 0.6698 (p90) REVERT: D 114 LYS cc_start: 0.9028 (tptt) cc_final: 0.8710 (tppp) REVERT: D 334 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6831 (tmt) REVERT: D 364 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8010 (mt0) REVERT: D 412 GLN cc_start: 0.7172 (tp-100) cc_final: 0.6891 (mm-40) outliers start: 48 outliers final: 21 residues processed: 117 average time/residue: 0.5056 time to fit residues: 65.3977 Evaluate side-chains 100 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.083563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.057859 restraints weight = 37476.243| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.39 r_work: 0.2889 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 0.043 13156 Z= 0.156 Angle : 0.706 11.280 17840 Z= 0.314 Chirality : 0.042 0.187 2084 Planarity : 0.004 0.027 2184 Dihedral : 14.538 175.152 2112 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.29 % Allowed : 19.99 % Favored : 76.72 % 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: 1.83 (0.22), residues: 1540 helix: 1.63 (0.17), residues: 996 sheet: 1.17 (0.47), residues: 116 loop : 0.41 (0.34), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 235 TYR 0.010 0.001 TYR C 170 PHE 0.005 0.001 PHE A 242 TRP 0.009 0.001 TRP B 176 HIS 0.002 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (13156) covalent geometry : angle 0.70628 / 0.31 (17840) hydrogen bonds : bond 0.03391 / 2.25 ( 796) hydrogen bonds : angle 4.09727 / 3.03 ( 2316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 71 time to evaluate : 0.421 Fit side-chains REVERT: A 13 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7945 (tt) REVERT: A 114 LYS cc_start: 0.9163 (tptt) cc_final: 0.8797 (tppp) REVERT: A 334 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7466 (tmt) REVERT: A 364 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7931 (mt0) REVERT: A 369 MET cc_start: 0.8930 (mmp) cc_final: 0.8710 (mmm) REVERT: B 13 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7643 (tt) REVERT: B 229 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8322 (tmtt) REVERT: B 277 LYS cc_start: 0.8677 (ptpp) cc_final: 0.8419 (pptt) REVERT: B 334 MET cc_start: 0.7920 (tmt) cc_final: 0.7396 (tmt) REVERT: B 364 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7947 (mt0) REVERT: B 369 MET cc_start: 0.8791 (mmp) cc_final: 0.8511 (mpm) REVERT: C 13 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7919 (tt) REVERT: C 114 LYS cc_start: 0.9212 (tptt) cc_final: 0.8825 (tppp) REVERT: C 364 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8290 (mm-40) REVERT: C 369 MET cc_start: 0.8774 (mmp) cc_final: 0.8457 (mpm) REVERT: D 13 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8266 (tt) REVERT: D 64 PHE cc_start: 0.7508 (m-10) cc_final: 0.6727 (p90) REVERT: D 114 LYS cc_start: 0.9097 (tptt) cc_final: 0.8751 (tppp) REVERT: D 364 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7992 (mt0) REVERT: D 412 GLN cc_start: 0.7261 (tp-100) cc_final: 0.6993 (mm-40) outliers start: 44 outliers final: 19 residues processed: 112 average time/residue: 0.5328 time to fit residues: 66.0262 Evaluate side-chains 92 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.083966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.058398 restraints weight = 37520.695| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.37 r_work: 0.2910 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13156 Z= 0.138 Angle : 0.709 11.675 17840 Z= 0.314 Chirality : 0.042 0.198 2084 Planarity : 0.003 0.024 2184 Dihedral : 14.176 177.899 2112 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.62 % Allowed : 21.03 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.22), residues: 1540 helix: 1.70 (0.17), residues: 976 sheet: 1.17 (0.47), residues: 116 loop : 0.37 (0.34), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 235 TYR 0.011 0.001 TYR C 170 PHE 0.005 0.001 PHE C 340 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13156) covalent geometry : angle 0.70891 / 0.31 (17840) hydrogen bonds : bond 0.03263 / 2.15 ( 796) hydrogen bonds : angle 4.10220 / 3.03 ( 2316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.512 Fit side-chains REVERT: A 13 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7938 (tt) REVERT: A 114 LYS cc_start: 0.9168 (tptt) cc_final: 0.8792 (tppp) REVERT: A 334 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7421 (tmt) REVERT: A 364 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7928 (mt0) REVERT: A 369 MET cc_start: 0.8971 (mmp) cc_final: 0.8734 (mmm) REVERT: B 13 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7684 (tt) REVERT: B 334 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7324 (tmt) REVERT: B 364 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7916 (mt0) REVERT: B 369 MET cc_start: 0.8819 (mmp) cc_final: 0.8544 (mpm) REVERT: C 13 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7915 (tt) REVERT: C 114 LYS cc_start: 0.9238 (tptt) cc_final: 0.8850 (tppp) REVERT: C 278 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7771 (tm-30) REVERT: C 364 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8266 (mm-40) REVERT: C 369 MET cc_start: 0.8798 (mmp) cc_final: 0.8481 (mpm) REVERT: D 13 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8260 (tt) REVERT: D 64 PHE cc_start: 0.7533 (m-10) cc_final: 0.6687 (p90) REVERT: D 114 LYS cc_start: 0.9109 (tptt) cc_final: 0.8743 (tppp) REVERT: D 364 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8038 (mt0) REVERT: D 412 GLN cc_start: 0.7194 (tp-100) cc_final: 0.6947 (mm-40) outliers start: 35 outliers final: 19 residues processed: 105 average time/residue: 0.5310 time to fit residues: 61.5031 Evaluate side-chains 95 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 99 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 2 optimal weight: 0.0170 chunk 61 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 116 optimal weight: 0.0030 chunk 31 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 overall best weight: 0.4828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.084841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.059730 restraints weight = 37608.904| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.39 r_work: 0.2938 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13156 Z= 0.124 Angle : 0.709 11.053 17840 Z= 0.314 Chirality : 0.042 0.185 2084 Planarity : 0.003 0.025 2184 Dihedral : 13.588 173.681 2112 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.25 % Allowed : 21.33 % Favored : 76.42 % 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: 1540 helix: 1.74 (0.17), residues: 996 sheet: 0.57 (0.47), residues: 128 loop : 0.60 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 111 TYR 0.011 0.001 TYR A 170 PHE 0.004 0.001 PHE D 309 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.000 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (13156) covalent geometry : angle 0.70918 / 0.31 (17840) hydrogen bonds : bond 0.03142 / 2.06 ( 796) hydrogen bonds : angle 4.05278 / 2.99 ( 2316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.450 Fit side-chains REVERT: A 114 LYS cc_start: 0.9154 (tptt) cc_final: 0.8766 (tppp) REVERT: A 334 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7395 (tmt) REVERT: A 364 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7934 (mt0) REVERT: A 369 MET cc_start: 0.8941 (mmp) cc_final: 0.8713 (mmm) REVERT: B 13 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7696 (tt) REVERT: B 235 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8137 (ttt-90) REVERT: B 277 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8420 (pptt) REVERT: B 334 MET cc_start: 0.7916 (tmt) cc_final: 0.7391 (tmt) REVERT: B 364 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7921 (mt0) REVERT: B 369 MET cc_start: 0.8831 (mmp) cc_final: 0.8557 (mpm) REVERT: C 13 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7919 (tt) REVERT: C 114 LYS cc_start: 0.9230 (tptt) cc_final: 0.8840 (tppp) REVERT: C 369 MET cc_start: 0.8786 (mmp) cc_final: 0.8473 (mpm) REVERT: D 13 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8240 (tt) REVERT: D 64 PHE cc_start: 0.7499 (m-10) cc_final: 0.6657 (p90) REVERT: D 114 LYS cc_start: 0.9139 (tptt) cc_final: 0.8746 (tppp) REVERT: D 364 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8042 (mt0) REVERT: D 412 GLN cc_start: 0.7223 (tp-100) cc_final: 0.6976 (mm-40) outliers start: 30 outliers final: 20 residues processed: 101 average time/residue: 0.5209 time to fit residues: 58.1193 Evaluate side-chains 94 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 148 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.084558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059329 restraints weight = 37664.850| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.38 r_work: 0.2928 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13156 Z= 0.133 Angle : 0.723 10.972 17840 Z= 0.320 Chirality : 0.042 0.190 2084 Planarity : 0.003 0.024 2184 Dihedral : 13.230 167.650 2112 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.17 % Allowed : 21.86 % 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: 1.93 (0.22), residues: 1540 helix: 1.74 (0.17), residues: 1000 sheet: 0.53 (0.47), residues: 128 loop : 0.59 (0.35), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 235 TYR 0.010 0.001 TYR C 170 PHE 0.004 0.001 PHE B 340 TRP 0.006 0.001 TRP B 176 HIS 0.002 0.000 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (13156) covalent geometry : angle 0.72301 / 0.32 (17840) hydrogen bonds : bond 0.03174 / 2.08 ( 796) hydrogen bonds : angle 4.05054 / 2.99 ( 2316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.476 Fit side-chains REVERT: A 114 LYS cc_start: 0.9153 (tptt) cc_final: 0.8759 (tppp) REVERT: A 334 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7408 (tmt) REVERT: A 364 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7943 (mt0) REVERT: A 369 MET cc_start: 0.8950 (mmp) cc_final: 0.8724 (mmm) REVERT: B 13 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7767 (tt) REVERT: B 277 LYS cc_start: 0.8642 (ptpp) cc_final: 0.8421 (pptt) REVERT: B 334 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7326 (tmt) REVERT: B 364 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7914 (mt0) REVERT: B 369 MET cc_start: 0.8859 (mmp) cc_final: 0.8560 (mmm) REVERT: C 13 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7931 (tt) REVERT: C 114 LYS cc_start: 0.9231 (tptt) cc_final: 0.8841 (tppp) REVERT: C 364 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8057 (mt0) REVERT: C 369 MET cc_start: 0.8805 (mmp) cc_final: 0.8497 (mpm) REVERT: D 13 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8249 (tt) REVERT: D 64 PHE cc_start: 0.7510 (m-10) cc_final: 0.6675 (p90) REVERT: D 114 LYS cc_start: 0.9157 (tptt) cc_final: 0.8763 (tppp) REVERT: D 364 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8055 (mt0) REVERT: D 412 GLN cc_start: 0.7210 (tp-100) cc_final: 0.6970 (mm-40) outliers start: 29 outliers final: 19 residues processed: 97 average time/residue: 0.5196 time to fit residues: 55.9929 Evaluate side-chains 92 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 10 optimal weight: 8.9990 chunk 71 optimal weight: 0.0040 chunk 48 optimal weight: 0.0070 chunk 128 optimal weight: 0.8980 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.085440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.060574 restraints weight = 37637.721| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.41 r_work: 0.2963 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13156 Z= 0.124 Angle : 0.721 10.730 17840 Z= 0.318 Chirality : 0.042 0.189 2084 Planarity : 0.003 0.024 2184 Dihedral : 12.676 168.047 2112 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.10 % Allowed : 21.78 % Favored : 76.12 % 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: 1.98 (0.22), residues: 1540 helix: 1.88 (0.17), residues: 976 sheet: 0.75 (0.47), residues: 124 loop : 0.34 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 235 TYR 0.010 0.001 TYR C 170 PHE 0.004 0.001 PHE B 366 TRP 0.005 0.001 TRP B 18 HIS 0.003 0.000 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (13156) covalent geometry : angle 0.72143 / 0.32 (17840) hydrogen bonds : bond 0.03054 / 2.00 ( 796) hydrogen bonds : angle 4.01568 / 2.96 ( 2316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4086.56 seconds wall clock time: 70 minutes 24.33 seconds (4224.33 seconds total)