Starting phenix.real_space_refine on Wed Feb 4 21:36:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nwk_49884/02_2026/9nwk_49884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nwk_49884/02_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_49884/02_2026/9nwk_49884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nwk_49884/02_2026/9nwk_49884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nwk_49884/02_2026/9nwk_49884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nwk_49884/02_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-2.0-5952/lib/python3.9/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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: 3.34, per 1000 atoms: 0.26 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: 1.14 Conformation dependent library (CDL) restraints added in 592.4 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: 0.45 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: 2.16 Time building geometry restraints manager: 1.49 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 - 1.94: 17378 1.94 - 3.88: 334 3.88 - 5.82: 84 5.82 - 7.76: 36 7.76 - 9.71: 8 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=" CG LYS B 303 " pdb=" CD LYS B 303 " pdb=" CE LYS B 303 " ideal model delta sigma weight residual 111.30 118.93 -7.63 2.30e+00 1.89e-01 1.10e+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: 36 106.25 - 141.67: 40 141.67 - 177.08: 20 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 - 0.039: 1486 0.039 - 0.078: 435 0.078 - 0.117: 141 0.117 - 0.156: 18 0.156 - 0.195: 4 Chirality restraints: 2084 Sorted by residual: chirality pdb=" C20 6OU A 504 " pdb=" C19 6OU A 504 " pdb=" C21 6OU A 504 " pdb=" O30 6OU A 504 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" C20 6OU C 504 " pdb=" C19 6OU C 504 " pdb=" C21 6OU C 504 " pdb=" O30 6OU C 504 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" C20 6OU D 501 " pdb=" C19 6OU D 501 " pdb=" C21 6OU D 501 " pdb=" O30 6OU D 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (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: 0.03 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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= 0.200 Angle : 0.739 9.706 17840 Z= 0.339 Chirality : 0.041 0.195 2084 Planarity : 0.004 0.025 2184 Dihedral : 22.689 177.083 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 covalent geometry : bond 0.00419 (13156) covalent geometry : angle 0.73874 (17840) hydrogen bonds : bond 0.14242 ( 796) hydrogen bonds : angle 5.74884 ( 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 : 0.553 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: 0.6826 time to fit residues: 77.1473 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 : 0.502 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.085680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.061928 restraints weight = 37108.150| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.18 r_work: 0.3036 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1056 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= 0.136 Angle : 0.640 9.967 17840 Z= 0.298 Chirality : 0.042 0.170 2084 Planarity : 0.004 0.024 2184 Dihedral : 20.890 163.769 2140 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.67 % Allowed : 19.76 % Favored : 76.57 % 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: 1.69 (0.22), residues: 1540 helix: 1.55 (0.16), residues: 996 sheet: 0.65 (0.47), residues: 112 loop : 0.43 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 235 TYR 0.008 0.001 TYR D 170 PHE 0.005 0.001 PHE A 242 TRP 0.007 0.001 TRP D 176 HIS 0.003 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00308 (13156) covalent geometry : angle 0.63954 (17840) hydrogen bonds : bond 0.03546 ( 796) hydrogen bonds : angle 4.50997 ( 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 131 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 82 time to evaluate : 0.392 Fit side-chains REVERT: A 114 LYS cc_start: 0.9019 (tptt) cc_final: 0.8786 (tppp) REVERT: A 235 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7730 (ttt-90) REVERT: A 316 HIS cc_start: 0.9404 (m90) cc_final: 0.8973 (m-70) REVERT: A 334 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7409 (tmt) REVERT: A 364 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7926 (mt0) REVERT: A 369 MET cc_start: 0.8849 (mmp) cc_final: 0.8552 (mpm) REVERT: B 229 LYS cc_start: 0.9016 (tppp) cc_final: 0.8516 (tmtt) REVERT: B 277 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8413 (ptpp) REVERT: B 334 MET cc_start: 0.7692 (tmt) cc_final: 0.7004 (tmt) REVERT: B 369 MET cc_start: 0.8625 (mmp) cc_final: 0.8243 (mpm) REVERT: C 114 LYS cc_start: 0.9215 (tptt) cc_final: 0.8753 (tppp) REVERT: C 289 MET cc_start: 0.9284 (mmm) cc_final: 0.8956 (mmm) REVERT: C 364 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8103 (tp-100) REVERT: C 369 MET cc_start: 0.8482 (mmp) cc_final: 0.8153 (mpm) REVERT: D 64 PHE cc_start: 0.7330 (m-10) cc_final: 0.6592 (p90) REVERT: D 114 LYS cc_start: 0.8890 (tptt) cc_final: 0.8653 (tppp) REVERT: D 316 HIS cc_start: 0.9325 (m90) cc_final: 0.8863 (m90) REVERT: D 342 ASN cc_start: 0.8788 (t0) cc_final: 0.8482 (t0) REVERT: D 364 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8101 (mt0) REVERT: D 412 GLN cc_start: 0.6910 (tp-100) cc_final: 0.6707 (mm-40) outliers start: 49 outliers final: 9 residues processed: 124 average time/residue: 0.5316 time to fit residues: 72.6581 Evaluate side-chains 83 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 28 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 389 LEU 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: 1.9990 chunk 125 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.082888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058144 restraints weight = 37745.025| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.19 r_work: 0.2928 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13156 Z= 0.188 Angle : 0.693 12.223 17840 Z= 0.318 Chirality : 0.043 0.163 2084 Planarity : 0.004 0.048 2184 Dihedral : 17.990 163.878 2119 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.49 % Allowed : 18.04 % Favored : 77.47 % 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: 1.63 (0.22), residues: 1540 helix: 1.48 (0.17), residues: 996 sheet: 0.96 (0.47), residues: 112 loop : 0.37 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 235 TYR 0.011 0.001 TYR A 170 PHE 0.008 0.001 PHE A 242 TRP 0.007 0.001 TRP A 176 HIS 0.002 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00434 (13156) covalent geometry : angle 0.69264 (17840) hydrogen bonds : bond 0.03910 ( 796) hydrogen bonds : angle 4.28958 ( 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 128 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 68 time to evaluate : 0.553 Fit side-chains REVERT: A 13 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8039 (tt) REVERT: A 30 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 114 LYS cc_start: 0.9162 (tptt) cc_final: 0.8823 (tppp) REVERT: A 334 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7415 (tmt) REVERT: A 364 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7990 (mt0) REVERT: A 369 MET cc_start: 0.8915 (mmp) cc_final: 0.8632 (mpm) REVERT: B 13 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7640 (tt) REVERT: B 334 MET cc_start: 0.7829 (tmt) cc_final: 0.7296 (tmt) REVERT: B 369 MET cc_start: 0.8768 (mmp) cc_final: 0.8377 (mpm) REVERT: C 13 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7908 (tt) REVERT: C 369 MET cc_start: 0.8671 (mmp) cc_final: 0.8352 (mpm) REVERT: D 30 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8636 (tt) REVERT: D 64 PHE cc_start: 0.7481 (m-10) cc_final: 0.6741 (p90) REVERT: D 114 LYS cc_start: 0.9123 (tptt) cc_final: 0.8819 (tppp) REVERT: D 364 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8138 (mt0) outliers start: 60 outliers final: 19 residues processed: 123 average time/residue: 0.5765 time to fit residues: 77.9619 Evaluate side-chains 89 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 106 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 195 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 338 VAL 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 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 30 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 277 LYS 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: 7.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3739 r_free = 0.3739 target = 0.084657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060541 restraints weight = 37618.833| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.19 r_work: 0.3005 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13156 Z= 0.127 Angle : 0.653 11.270 17840 Z= 0.299 Chirality : 0.041 0.154 2084 Planarity : 0.003 0.025 2184 Dihedral : 16.843 163.771 2113 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.19 % Allowed : 18.19 % Favored : 77.62 % 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: 1.75 (0.22), residues: 1540 helix: 1.54 (0.17), residues: 992 sheet: 1.28 (0.47), residues: 116 loop : 0.42 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 235 TYR 0.012 0.001 TYR C 170 PHE 0.006 0.001 PHE A 302 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00291 (13156) covalent geometry : angle 0.65287 (17840) hydrogen bonds : bond 0.03303 ( 796) hydrogen bonds : angle 4.16562 ( 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 126 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 70 time to evaluate : 0.531 Fit side-chains REVERT: A 114 LYS cc_start: 0.9181 (tptt) cc_final: 0.8834 (tppp) REVERT: A 151 ILE cc_start: 0.9159 (mm) cc_final: 0.8916 (mp) REVERT: A 334 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7371 (tmt) REVERT: A 364 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8039 (mt0) REVERT: B 13 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7659 (tt) REVERT: B 229 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8534 (tmtt) REVERT: B 277 LYS cc_start: 0.8631 (pptt) cc_final: 0.8405 (ptpp) REVERT: B 334 MET cc_start: 0.7808 (tmt) cc_final: 0.7041 (tmt) REVERT: B 364 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8104 (mt0) REVERT: B 369 MET cc_start: 0.8720 (mmp) cc_final: 0.8422 (mpm) REVERT: C 13 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7930 (tt) REVERT: C 114 LYS cc_start: 0.9298 (tptt) cc_final: 0.8805 (tppp) REVERT: C 364 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8295 (mt0) REVERT: C 369 MET cc_start: 0.8670 (mmp) cc_final: 0.8380 (mpm) REVERT: D 13 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8306 (tt) REVERT: D 64 PHE cc_start: 0.7420 (m-10) cc_final: 0.6636 (p90) REVERT: D 114 LYS cc_start: 0.9121 (tptt) cc_final: 0.8801 (tppp) REVERT: D 364 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8207 (mt0) outliers start: 56 outliers final: 20 residues processed: 120 average time/residue: 0.5414 time to fit residues: 71.8928 Evaluate side-chains 90 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 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 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 26 TYR 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: 8.9990 chunk 88 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3697 r_free = 0.3697 target = 0.084111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058539 restraints weight = 37777.123| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.38 r_work: 0.2908 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13156 Z= 0.136 Angle : 0.656 11.672 17840 Z= 0.300 Chirality : 0.041 0.209 2084 Planarity : 0.003 0.025 2184 Dihedral : 16.354 164.526 2113 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.12 % Allowed : 19.31 % Favored : 76.57 % 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: 1.85 (0.22), residues: 1540 helix: 1.61 (0.17), residues: 988 sheet: 1.30 (0.47), residues: 116 loop : 0.49 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.010 0.001 TYR C 170 PHE 0.005 0.001 PHE D 302 TRP 0.006 0.001 TRP D 176 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00317 (13156) covalent geometry : angle 0.65552 (17840) hydrogen bonds : bond 0.03293 ( 796) hydrogen bonds : angle 4.10979 ( 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 123 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 68 time to evaluate : 0.528 Fit side-chains REVERT: A 13 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7928 (tt) REVERT: A 110 VAL cc_start: 0.9296 (m) cc_final: 0.9075 (p) REVERT: A 114 LYS cc_start: 0.9112 (tptt) cc_final: 0.8792 (tppp) REVERT: A 238 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8333 (ttp80) REVERT: A 334 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7495 (tmt) REVERT: A 364 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7891 (mt0) REVERT: A 369 MET cc_start: 0.8782 (mmm) cc_final: 0.8446 (mpm) REVERT: B 13 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7596 (tt) REVERT: B 229 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8330 (tmtt) REVERT: B 277 LYS cc_start: 0.8553 (pptt) cc_final: 0.8296 (ptpp) REVERT: B 334 MET cc_start: 0.7846 (tmt) cc_final: 0.7078 (tmt) REVERT: B 364 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7919 (mt0) REVERT: B 369 MET cc_start: 0.8732 (mmp) cc_final: 0.8433 (mpm) REVERT: C 13 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7860 (tt) REVERT: C 114 LYS cc_start: 0.9221 (tptt) cc_final: 0.8791 (tppp) REVERT: C 364 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8141 (mt0) REVERT: C 369 MET cc_start: 0.8712 (mmp) cc_final: 0.8423 (mpm) REVERT: D 13 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8250 (tt) REVERT: D 24 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8688 (mp) REVERT: D 30 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8441 (tt) REVERT: D 64 PHE cc_start: 0.7586 (m-10) cc_final: 0.6696 (p90) REVERT: D 114 LYS cc_start: 0.9035 (tptt) cc_final: 0.8708 (tppp) REVERT: D 364 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7996 (mt0) outliers start: 55 outliers final: 21 residues processed: 119 average time/residue: 0.5561 time to fit residues: 72.8271 Evaluate side-chains 96 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 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 30 ILE 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 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3699 r_free = 0.3699 target = 0.084148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.058752 restraints weight = 37480.346| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.37 r_work: 0.2917 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13156 Z= 0.131 Angle : 0.654 12.075 17840 Z= 0.300 Chirality : 0.041 0.188 2084 Planarity : 0.003 0.024 2184 Dihedral : 15.826 163.619 2113 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.22 % Allowed : 20.28 % Favored : 76.50 % 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: 1.90 (0.22), residues: 1540 helix: 1.66 (0.17), residues: 988 sheet: 1.24 (0.47), residues: 116 loop : 0.51 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.010 0.001 TYR C 170 PHE 0.005 0.001 PHE C 340 TRP 0.005 0.001 TRP B 176 HIS 0.003 0.000 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00305 (13156) covalent geometry : angle 0.65374 (17840) hydrogen bonds : bond 0.03201 ( 796) hydrogen bonds : angle 4.06503 ( 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 112 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 69 time to evaluate : 0.411 Fit side-chains REVERT: A 13 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7933 (tt) REVERT: A 114 LYS cc_start: 0.9120 (tptt) cc_final: 0.8784 (tppp) REVERT: A 334 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7468 (tmt) REVERT: A 364 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7922 (mt0) REVERT: B 229 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8330 (tmtt) REVERT: B 277 LYS cc_start: 0.8603 (pptt) cc_final: 0.8346 (ptpt) REVERT: B 334 MET cc_start: 0.7896 (tmt) cc_final: 0.7129 (tmt) REVERT: B 364 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7900 (mt0) REVERT: B 369 MET cc_start: 0.8770 (mmp) cc_final: 0.8505 (mpm) REVERT: C 114 LYS cc_start: 0.9221 (tptt) cc_final: 0.8788 (tppp) REVERT: C 364 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8087 (mt0) REVERT: C 369 MET cc_start: 0.8740 (mmp) cc_final: 0.8448 (mpm) REVERT: D 24 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8654 (mp) REVERT: D 64 PHE cc_start: 0.7531 (m-10) cc_final: 0.6647 (p90) REVERT: D 114 LYS cc_start: 0.9062 (tptt) cc_final: 0.8714 (tppp) REVERT: D 334 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6823 (tmt) REVERT: D 364 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8063 (mt0) REVERT: D 412 GLN cc_start: 0.7222 (tp-100) cc_final: 0.6956 (mm-40) outliers start: 43 outliers final: 23 residues processed: 107 average time/residue: 0.4964 time to fit residues: 58.8435 Evaluate side-chains 91 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 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 109 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 26 TYR Chi-restraints excluded: chain B residue 112 LEU 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 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 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 292 HIS 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: 1.9990 chunk 133 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 113 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.083048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057159 restraints weight = 37578.022| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.38 r_work: 0.2863 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13156 Z= 0.166 Angle : 0.690 11.806 17840 Z= 0.315 Chirality : 0.042 0.195 2084 Planarity : 0.004 0.027 2184 Dihedral : 15.628 164.106 2113 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.14 % Allowed : 20.73 % 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: 1.82 (0.22), residues: 1540 helix: 1.60 (0.17), residues: 992 sheet: 1.11 (0.47), residues: 112 loop : 0.50 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 29 TYR 0.010 0.001 TYR A 170 PHE 0.006 0.001 PHE A 242 TRP 0.008 0.001 TRP A 176 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00389 (13156) covalent geometry : angle 0.69020 (17840) hydrogen bonds : bond 0.03468 ( 796) hydrogen bonds : angle 4.11012 ( 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 112 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 0.524 Fit side-chains REVERT: A 13 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7996 (tt) REVERT: A 114 LYS cc_start: 0.9188 (tptt) cc_final: 0.8818 (tppp) REVERT: A 334 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7435 (tmt) REVERT: A 364 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7933 (mt0) REVERT: A 369 MET cc_start: 0.8873 (mmm) cc_final: 0.8561 (mpm) REVERT: B 13 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7712 (tt) REVERT: B 277 LYS cc_start: 0.8670 (pptt) cc_final: 0.8392 (ptpt) REVERT: B 334 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7130 (tmt) REVERT: B 369 MET cc_start: 0.8819 (mmp) cc_final: 0.8573 (mpm) REVERT: C 13 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7979 (tt) REVERT: C 114 LYS cc_start: 0.9256 (tptt) cc_final: 0.8873 (tppp) REVERT: C 364 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8274 (mm-40) REVERT: C 369 MET cc_start: 0.8831 (mmp) cc_final: 0.8535 (mpm) REVERT: D 13 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8253 (tt) REVERT: D 24 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8638 (mp) REVERT: D 64 PHE cc_start: 0.7508 (m-10) cc_final: 0.6704 (p90) REVERT: D 114 LYS cc_start: 0.9142 (tptt) cc_final: 0.8749 (tppp) REVERT: D 364 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8048 (mt0) REVERT: D 412 GLN cc_start: 0.7247 (tp-100) cc_final: 0.7009 (mm-40) outliers start: 42 outliers final: 21 residues processed: 108 average time/residue: 0.4820 time to fit residues: 57.8703 Evaluate side-chains 95 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 112 LEU 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 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 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: 10.0000 chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.083849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.058192 restraints weight = 37568.432| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.37 r_work: 0.2896 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2949 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= 0.136 Angle : 0.682 11.756 17840 Z= 0.311 Chirality : 0.042 0.199 2084 Planarity : 0.003 0.025 2184 Dihedral : 15.289 164.127 2113 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.84 % Allowed : 21.41 % Favored : 75.75 % 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: 1.86 (0.22), residues: 1540 helix: 1.62 (0.17), residues: 992 sheet: 1.22 (0.46), residues: 116 loop : 0.52 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 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 0.000 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00320 (13156) covalent geometry : angle 0.68240 (17840) hydrogen bonds : bond 0.03242 ( 796) hydrogen bonds : angle 4.08743 ( 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 102 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 0.518 Fit side-chains REVERT: A 13 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8007 (tt) REVERT: A 114 LYS cc_start: 0.9199 (tptt) cc_final: 0.8808 (tppp) REVERT: A 334 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7430 (tmt) REVERT: A 364 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7922 (mt0) REVERT: B 13 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7706 (tt) REVERT: B 277 LYS cc_start: 0.8636 (pptt) cc_final: 0.8347 (ptpt) REVERT: B 334 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7355 (tmt) REVERT: B 364 GLN cc_start: 0.8460 (mm-40) cc_final: 0.7948 (mt0) REVERT: B 369 MET cc_start: 0.8845 (mmp) cc_final: 0.8599 (mpm) REVERT: C 13 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7962 (tt) REVERT: C 114 LYS cc_start: 0.9224 (tptt) cc_final: 0.8844 (tppp) REVERT: C 369 MET cc_start: 0.8849 (mmp) cc_final: 0.8559 (mpm) REVERT: D 13 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8259 (tt) REVERT: D 64 PHE cc_start: 0.7520 (m-10) cc_final: 0.6660 (p90) REVERT: D 114 LYS cc_start: 0.9148 (tptt) cc_final: 0.8752 (tppp) REVERT: D 334 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.6838 (tmt) REVERT: D 364 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8057 (mt0) REVERT: D 412 GLN cc_start: 0.7246 (tp-100) cc_final: 0.7013 (mm-40) outliers start: 38 outliers final: 21 residues processed: 99 average time/residue: 0.4883 time to fit residues: 53.9114 Evaluate side-chains 92 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 112 LEU 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 112 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 334 MET 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: 2.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 116 optimal weight: 0.0670 chunk 31 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.084602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059230 restraints weight = 37673.536| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.39 r_work: 0.2933 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3015 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= 0.128 Angle : 0.689 12.893 17840 Z= 0.311 Chirality : 0.041 0.189 2084 Planarity : 0.003 0.025 2184 Dihedral : 14.814 164.556 2113 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.54 % Allowed : 21.93 % Favored : 75.52 % 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: 1.91 (0.22), residues: 1540 helix: 1.69 (0.17), residues: 996 sheet: 1.28 (0.48), residues: 116 loop : 0.41 (0.34), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.010 0.001 TYR C 170 PHE 0.006 0.001 PHE C 365 TRP 0.006 0.001 TRP D 264 HIS 0.003 0.000 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00297 (13156) covalent geometry : angle 0.68919 (17840) hydrogen bonds : bond 0.03128 ( 796) hydrogen bonds : angle 4.02255 ( 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 98 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.519 Fit side-chains REVERT: A 13 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8089 (tt) REVERT: A 114 LYS cc_start: 0.9200 (tptt) cc_final: 0.8812 (tppp) REVERT: A 334 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7388 (tmt) REVERT: A 364 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7939 (mt0) REVERT: A 369 MET cc_start: 0.8906 (mmm) cc_final: 0.8606 (mpm) REVERT: B 13 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7809 (tt) REVERT: B 277 LYS cc_start: 0.8595 (pptt) cc_final: 0.8265 (ptpp) REVERT: B 334 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7360 (tmt) REVERT: B 364 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7943 (mt0) REVERT: B 369 MET cc_start: 0.8861 (mmp) cc_final: 0.8623 (mpm) REVERT: C 13 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7971 (tt) REVERT: C 114 LYS cc_start: 0.9229 (tptt) cc_final: 0.8853 (tppp) REVERT: C 364 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8064 (mt0) REVERT: C 369 MET cc_start: 0.8844 (mmp) cc_final: 0.8569 (mpm) REVERT: D 13 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8259 (tt) REVERT: D 64 PHE cc_start: 0.7522 (m-10) cc_final: 0.6674 (p90) REVERT: D 114 LYS cc_start: 0.9119 (tptt) cc_final: 0.8776 (tppp) REVERT: D 278 GLU cc_start: 0.8202 (pp20) cc_final: 0.7846 (tm-30) REVERT: D 364 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8069 (mt0) outliers start: 34 outliers final: 21 residues processed: 95 average time/residue: 0.5340 time to fit residues: 56.1556 Evaluate side-chains 88 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 310 ILE 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 276 LEU 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 44 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 0.0370 chunk 8 optimal weight: 0.3980 chunk 148 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.084488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.059148 restraints weight = 37730.762| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.38 r_work: 0.2925 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13156 Z= 0.130 Angle : 0.700 12.181 17840 Z= 0.315 Chirality : 0.041 0.187 2084 Planarity : 0.003 0.025 2184 Dihedral : 14.611 164.391 2113 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.32 % Allowed : 22.31 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.22), residues: 1540 helix: 1.72 (0.17), residues: 996 sheet: 0.91 (0.47), residues: 124 loop : 0.48 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 235 TYR 0.010 0.001 TYR C 170 PHE 0.005 0.001 PHE A 397 TRP 0.006 0.001 TRP A 176 HIS 0.002 0.000 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00304 (13156) covalent geometry : angle 0.69999 (17840) hydrogen bonds : bond 0.03120 ( 796) hydrogen bonds : angle 4.00262 ( 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 94 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.547 Fit side-chains REVERT: A 114 LYS cc_start: 0.9186 (tptt) cc_final: 0.8787 (tppp) REVERT: A 334 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7390 (tmt) REVERT: A 364 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7952 (mt0) REVERT: A 369 MET cc_start: 0.8923 (mmm) cc_final: 0.8618 (mpm) REVERT: B 13 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7829 (tt) REVERT: B 277 LYS cc_start: 0.8599 (pptt) cc_final: 0.8269 (ptpp) REVERT: B 334 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7353 (tmt) REVERT: B 364 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7939 (mt0) REVERT: B 369 MET cc_start: 0.8882 (mmp) cc_final: 0.8606 (mpm) REVERT: C 13 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7962 (tt) REVERT: C 114 LYS cc_start: 0.9222 (tptt) cc_final: 0.8840 (tppp) REVERT: C 277 LYS cc_start: 0.9377 (mtmm) cc_final: 0.9176 (mtmt) REVERT: C 364 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8019 (mt0) REVERT: C 369 MET cc_start: 0.8849 (mmp) cc_final: 0.8566 (mpm) REVERT: D 13 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8261 (tt) REVERT: D 64 PHE cc_start: 0.7534 (m-10) cc_final: 0.6686 (p90) REVERT: D 114 LYS cc_start: 0.9115 (tptt) cc_final: 0.8754 (tppp) REVERT: D 278 GLU cc_start: 0.8231 (pp20) cc_final: 0.7999 (tm-30) REVERT: D 364 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8080 (mt0) outliers start: 31 outliers final: 21 residues processed: 92 average time/residue: 0.5120 time to fit residues: 52.2441 Evaluate side-chains 87 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 195 THR Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 ILE 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 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 292 HIS 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: 0.7980 chunk 69 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.084308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058928 restraints weight = 37514.722| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.39 r_work: 0.2923 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3158 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= 0.132 Angle : 0.702 12.188 17840 Z= 0.317 Chirality : 0.041 0.188 2084 Planarity : 0.003 0.024 2184 Dihedral : 14.545 164.459 2113 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.40 % Allowed : 22.16 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.22), residues: 1540 helix: 1.73 (0.17), residues: 996 sheet: 0.91 (0.47), residues: 124 loop : 0.47 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 235 TYR 0.010 0.001 TYR C 170 PHE 0.004 0.001 PHE B 366 TRP 0.006 0.001 TRP A 176 HIS 0.003 0.000 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00310 (13156) covalent geometry : angle 0.70222 (17840) hydrogen bonds : bond 0.03116 ( 796) hydrogen bonds : angle 3.98638 ( 2316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.59 seconds wall clock time: 73 minutes 32.43 seconds (4412.43 seconds total)