Starting phenix.real_space_refine on Mon May 4 09:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9quw_53384/05_2026/9quw_53384_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9quw_53384/05_2026/9quw_53384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9quw_53384/05_2026/9quw_53384_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9quw_53384/05_2026/9quw_53384_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9quw_53384/05_2026/9quw_53384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9quw_53384/05_2026/9quw_53384.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 C 8410 2.51 5 N 2090 2.21 5 O 2412 1.98 5 H 7044 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20024 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1521 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "D" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Chain breaks: 2 Chain: "F" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Chain breaks: 2 Chain: "A" Number of atoms: 6828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6828 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain: "B" Number of atoms: 6828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6828 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain: "C" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1521 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G50': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G50': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.08, per 1000 atoms: 0.20 Number of scatterers: 20024 At special positions: 0 Unit cell: (83.2, 116.35, 137.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 2 15.00 O 2412 8.00 N 2090 7.00 C 8410 6.00 H 7044 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 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: 1.97 Conformation dependent library (CDL) restraints added in 520.6 milliseconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 22 sheets defined 49.5% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.633A pdb=" N ILE E 83 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.601A pdb=" N LEU E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.616A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.971A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 removed outlier: 3.601A pdb=" N SER D 169 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.632A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.890A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 169 removed outlier: 3.557A pdb=" N SER F 168 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 169 " --> pdb=" O SER F 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 165 through 169' Processing helix chain 'A' and resid 82 through 106 Processing helix chain 'A' and resid 113 through 135 removed outlier: 3.590A pdb=" N ILE A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.843A pdb=" N GLY A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 169 through 192 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 201 through 226 removed outlier: 3.614A pdb=" N VAL A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 245 through 260 Proline residue: A 251 - end of helix Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 277 through 295 removed outlier: 3.710A pdb=" N LEU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 325 Processing helix chain 'A' and resid 334 through 357 Processing helix chain 'A' and resid 361 through 379 removed outlier: 3.634A pdb=" N LEU A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 408 removed outlier: 4.398A pdb=" N VAL A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Proline residue: A 398 - end of helix removed outlier: 3.647A pdb=" N VAL A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 469 through 479 Processing helix chain 'A' and resid 480 through 517 Proline residue: A 503 - end of helix Proline residue: A 514 - end of helix Processing helix chain 'B' and resid 82 through 106 Processing helix chain 'B' and resid 113 through 135 removed outlier: 3.590A pdb=" N ILE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.843A pdb=" N GLY B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 169 through 192 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 201 through 226 removed outlier: 3.614A pdb=" N VAL B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 230 through 241 Processing helix chain 'B' and resid 245 through 260 Proline residue: B 251 - end of helix Processing helix chain 'B' and resid 266 through 275 Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.709A pdb=" N LEU B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 325 Processing helix chain 'B' and resid 334 through 357 Processing helix chain 'B' and resid 361 through 379 removed outlier: 3.634A pdb=" N LEU B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 408 removed outlier: 4.398A pdb=" N VAL B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) Proline residue: B 398 - end of helix removed outlier: 3.647A pdb=" N VAL B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 440 Processing helix chain 'B' and resid 446 through 456 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 469 through 479 Processing helix chain 'B' and resid 480 through 517 Proline residue: B 503 - end of helix Proline residue: B 514 - end of helix Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.632A pdb=" N ILE C 83 " --> pdb=" O GLN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 removed outlier: 3.601A pdb=" N LEU C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 182 through 188 Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.752A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.539A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.612A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 116 through 118 removed outlier: 5.671A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.706A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AB2, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AB3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.504A pdb=" N TRP F 47 " --> pdb=" O LYS F 38 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 145 through 146 Processing sheet with id=AB7, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AB8, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.753A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 67 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.539A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.612A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 116 through 118 removed outlier: 5.671A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 147 through 148 752 hydrogen bonds defined for protein. 2133 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: 4.54 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7024 1.03 - 1.23: 63 1.23 - 1.42: 5373 1.42 - 1.62: 7758 1.62 - 1.82: 94 Bond restraints: 20312 Sorted by residual: bond pdb=" O5 LPP A 601 " pdb=" P1 LPP A 601 " ideal model delta sigma weight residual 2.278 1.620 0.658 2.00e-02 2.50e+03 1.08e+03 bond pdb=" O5 LPP B 601 " pdb=" P1 LPP B 601 " ideal model delta sigma weight residual 2.278 1.621 0.657 2.00e-02 2.50e+03 1.08e+03 bond pdb=" O4 LPP B 601 " pdb=" P1 LPP B 601 " ideal model delta sigma weight residual 1.764 1.515 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" O4 LPP A 601 " pdb=" P1 LPP A 601 " ideal model delta sigma weight residual 1.764 1.516 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C6 LPP B 601 " pdb=" O5 LPP B 601 " ideal model delta sigma weight residual 1.243 1.456 -0.213 2.00e-02 2.50e+03 1.14e+02 ... (remaining 20307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.75: 34008 8.75 - 17.51: 2 17.51 - 26.26: 2 26.26 - 35.02: 2 35.02 - 43.77: 4 Bond angle restraints: 34018 Sorted by residual: angle pdb=" O4 LPP A 601 " pdb=" P1 LPP A 601 " pdb=" O5 LPP A 601 " ideal model delta sigma weight residual 62.99 106.76 -43.77 3.00e+00 1.11e-01 2.13e+02 angle pdb=" O4 LPP B 601 " pdb=" P1 LPP B 601 " pdb=" O5 LPP B 601 " ideal model delta sigma weight residual 62.99 106.76 -43.77 3.00e+00 1.11e-01 2.13e+02 angle pdb=" C6 LPP A 601 " pdb=" O5 LPP A 601 " pdb=" P1 LPP A 601 " ideal model delta sigma weight residual 82.33 119.62 -37.29 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C6 LPP B 601 " pdb=" O5 LPP B 601 " pdb=" P1 LPP B 601 " ideal model delta sigma weight residual 82.33 119.55 -37.22 3.00e+00 1.11e-01 1.54e+02 angle pdb=" O2 LPP B 601 " pdb=" P1 LPP B 601 " pdb=" O3 LPP B 601 " ideal model delta sigma weight residual 142.11 111.91 30.20 3.00e+00 1.11e-01 1.01e+02 ... (remaining 34013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8940 17.98 - 35.96: 924 35.96 - 53.94: 347 53.94 - 71.92: 93 71.92 - 89.90: 6 Dihedral angle restraints: 10310 sinusoidal: 5076 harmonic: 5234 Sorted by residual: dihedral pdb=" CD ARG C 24 " pdb=" NE ARG C 24 " pdb=" CZ ARG C 24 " pdb=" NH1 ARG C 24 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CD ARG E 24 " pdb=" NE ARG E 24 " pdb=" CZ ARG E 24 " pdb=" NH1 ARG E 24 " ideal model delta sinusoidal sigma weight residual 0.00 89.82 -89.82 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS D 148 " pdb=" SG CYS D 148 " pdb=" SG CYS D 203 " pdb=" CB CYS D 203 " ideal model delta sinusoidal sigma weight residual 93.00 150.70 -57.70 1 1.00e+01 1.00e-02 4.47e+01 ... (remaining 10307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1710 0.046 - 0.093: 318 0.093 - 0.139: 76 0.139 - 0.185: 6 0.185 - 0.232: 2 Chirality restraints: 2112 Sorted by residual: chirality pdb=" C7 LPP B 601 " pdb=" C6 LPP B 601 " pdb=" C8 LPP B 601 " pdb=" O9 LPP B 601 " both_signs ideal model delta sigma weight residual False -2.69 -2.46 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C7 LPP A 601 " pdb=" C6 LPP A 601 " pdb=" C8 LPP A 601 " pdb=" O9 LPP A 601 " both_signs ideal model delta sigma weight residual False -2.69 -2.46 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ARG E 24 " pdb=" N ARG E 24 " pdb=" C ARG E 24 " pdb=" CB ARG E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 2109 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 24 " -1.107 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG C 24 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG C 24 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 24 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG C 24 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 24 " -1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG E 24 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG E 24 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG E 24 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG E 24 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 181 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C ASP D 181 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP D 181 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU D 182 " 0.014 2.00e-02 2.50e+03 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1069 2.22 - 2.81: 31881 2.81 - 3.41: 46252 3.41 - 4.00: 62217 4.00 - 4.60: 97203 Nonbonded interactions: 238622 Sorted by model distance: nonbonded pdb=" OE1 GLU B 215 " pdb="HH11 ARG B 432 " model vdw 1.620 2.450 nonbonded pdb=" OE1 GLU A 215 " pdb="HH11 ARG A 432 " model vdw 1.621 2.450 nonbonded pdb=" HE2 MET B 209 " pdb="HD13 LEU B 281 " model vdw 1.814 2.440 nonbonded pdb=" HE2 MET A 209 " pdb="HD13 LEU A 281 " model vdw 1.814 2.440 nonbonded pdb=" H SER A 252 " pdb=" HG SER A 252 " model vdw 1.916 2.100 ... (remaining 238617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.540 Find NCS groups from input model: 0.230 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:7.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.011 0.658 13276 Z= 0.522 Angle : 0.952 43.775 18040 Z= 0.407 Chirality : 0.040 0.232 2112 Planarity : 0.015 0.496 2222 Dihedral : 16.463 89.898 4748 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.07 % Allowed : 25.70 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.22), residues: 1672 helix: 2.22 (0.19), residues: 768 sheet: -0.43 (0.31), residues: 356 loop : -1.59 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 414 TYR 0.015 0.001 TYR F 110 PHE 0.027 0.001 PHE B 327 TRP 0.011 0.001 TRP B 233 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.01058 (13268) covalent geometry : angle 0.95173 (18024) SS BOND : bond 0.00153 ( 8) SS BOND : angle 0.82571 ( 16) hydrogen bonds : bond 0.14702 ( 726) hydrogen bonds : angle 6.41532 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 GLU cc_start: 0.7781 (mp0) cc_final: 0.7197 (mp0) REVERT: E 107 LYS cc_start: 0.8910 (tptt) cc_final: 0.8663 (tppp) REVERT: E 192 TYR cc_start: 0.7149 (m-10) cc_final: 0.6570 (m-10) REVERT: D 46 GLU cc_start: 0.9238 (tt0) cc_final: 0.8745 (tt0) REVERT: D 62 GLU cc_start: 0.8627 (mp0) cc_final: 0.8395 (mp0) REVERT: F 62 GLU cc_start: 0.8541 (mp0) cc_final: 0.8283 (mp0) REVERT: F 215 ASP cc_start: 0.7857 (m-30) cc_final: 0.7312 (t70) REVERT: B 301 PHE cc_start: 0.7991 (t80) cc_final: 0.7577 (t80) REVERT: C 79 GLU cc_start: 0.7356 (mp0) cc_final: 0.6821 (mp0) REVERT: C 105 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7406 (tm-30) REVERT: C 192 TYR cc_start: 0.6235 (m-10) cc_final: 0.5762 (m-10) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.9126 time to fit residues: 142.5979 Evaluate side-chains 129 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.106550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074692 restraints weight = 58230.337| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.30 r_work: 0.2970 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13276 Z= 0.201 Angle : 0.549 5.470 18040 Z= 0.292 Chirality : 0.039 0.167 2112 Planarity : 0.004 0.081 2222 Dihedral : 7.590 56.850 1882 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.57 % Allowed : 24.30 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1672 helix: 2.12 (0.19), residues: 776 sheet: -0.33 (0.29), residues: 370 loop : -1.53 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 414 TYR 0.009 0.001 TYR E 86 PHE 0.024 0.001 PHE B 327 TRP 0.011 0.001 TRP B 98 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00450 (13268) covalent geometry : angle 0.54895 (18024) SS BOND : bond 0.00353 ( 8) SS BOND : angle 0.80977 ( 16) hydrogen bonds : bond 0.04917 ( 726) hydrogen bonds : angle 4.96757 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.7341 (mtm) REVERT: E 79 GLU cc_start: 0.7704 (mp0) cc_final: 0.7051 (mp0) REVERT: E 107 LYS cc_start: 0.8901 (tptt) cc_final: 0.8603 (tppp) REVERT: D 62 GLU cc_start: 0.8549 (mp0) cc_final: 0.8277 (mp0) REVERT: D 108 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.6190 (mmt) REVERT: D 216 LYS cc_start: 0.7402 (tptt) cc_final: 0.7153 (tppt) REVERT: F 13 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8325 (mttm) REVERT: F 62 GLU cc_start: 0.8567 (mp0) cc_final: 0.8252 (mp0) REVERT: C 4 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.7393 (mtm) REVERT: C 79 GLU cc_start: 0.7308 (mp0) cc_final: 0.6796 (mp0) outliers start: 51 outliers final: 23 residues processed: 172 average time/residue: 0.7982 time to fit residues: 152.0602 Evaluate side-chains 162 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 134 CYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 151 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 158 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.075311 restraints weight = 58256.440| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.30 r_work: 0.2986 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13276 Z= 0.149 Angle : 0.498 4.961 18040 Z= 0.263 Chirality : 0.038 0.136 2112 Planarity : 0.003 0.041 2222 Dihedral : 6.385 56.747 1882 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.29 % Allowed : 24.65 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.22), residues: 1672 helix: 2.24 (0.19), residues: 778 sheet: -0.42 (0.29), residues: 370 loop : -1.51 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 414 TYR 0.011 0.001 TYR E 86 PHE 0.019 0.001 PHE B 327 TRP 0.011 0.001 TRP B 98 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00335 (13268) covalent geometry : angle 0.49791 (18024) SS BOND : bond 0.00155 ( 8) SS BOND : angle 0.61107 ( 16) hydrogen bonds : bond 0.04428 ( 726) hydrogen bonds : angle 4.57808 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.7381 (mtm) REVERT: E 79 GLU cc_start: 0.7748 (mp0) cc_final: 0.7116 (mp0) REVERT: E 107 LYS cc_start: 0.8871 (tptt) cc_final: 0.8566 (tppp) REVERT: D 62 GLU cc_start: 0.8563 (mp0) cc_final: 0.8305 (mp0) REVERT: D 216 LYS cc_start: 0.7427 (tptt) cc_final: 0.7132 (tppt) REVERT: F 13 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8334 (mttm) REVERT: F 62 GLU cc_start: 0.8586 (mp0) cc_final: 0.8296 (mp0) REVERT: F 215 ASP cc_start: 0.7793 (m-30) cc_final: 0.7227 (t70) REVERT: C 4 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.7380 (mtm) REVERT: C 24 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7930 (ttm-80) REVERT: C 79 GLU cc_start: 0.7403 (mp0) cc_final: 0.6827 (mp0) outliers start: 47 outliers final: 16 residues processed: 174 average time/residue: 0.8186 time to fit residues: 158.0170 Evaluate side-chains 160 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 147 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.105982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073633 restraints weight = 58279.122| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.19 r_work: 0.2967 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13276 Z= 0.185 Angle : 0.526 5.973 18040 Z= 0.276 Chirality : 0.038 0.154 2112 Planarity : 0.004 0.041 2222 Dihedral : 6.255 59.420 1882 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.64 % Allowed : 24.86 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1672 helix: 2.30 (0.19), residues: 778 sheet: -0.49 (0.29), residues: 370 loop : -1.51 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 414 TYR 0.011 0.001 TYR E 86 PHE 0.023 0.001 PHE B 327 TRP 0.011 0.001 TRP B 98 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00418 (13268) covalent geometry : angle 0.52569 (18024) SS BOND : bond 0.00198 ( 8) SS BOND : angle 0.72083 ( 16) hydrogen bonds : bond 0.04409 ( 726) hydrogen bonds : angle 4.48218 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.7380 (mtm) REVERT: E 79 GLU cc_start: 0.7678 (mp0) cc_final: 0.7070 (mp0) REVERT: E 105 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6968 (tm-30) REVERT: E 107 LYS cc_start: 0.8854 (tptt) cc_final: 0.8593 (tppp) REVERT: D 62 GLU cc_start: 0.8562 (mp0) cc_final: 0.8294 (mp0) REVERT: D 108 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.6159 (mmt) REVERT: D 171 VAL cc_start: 0.9458 (OUTLIER) cc_final: 0.9252 (t) REVERT: D 216 LYS cc_start: 0.7419 (tptt) cc_final: 0.7188 (tppt) REVERT: F 13 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8381 (mttm) REVERT: F 62 GLU cc_start: 0.8578 (mp0) cc_final: 0.8278 (mp0) REVERT: F 108 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.6680 (mmt) REVERT: F 215 ASP cc_start: 0.7762 (m-30) cc_final: 0.7200 (t70) REVERT: C 4 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.7367 (mtm) REVERT: C 79 GLU cc_start: 0.7452 (mp0) cc_final: 0.6855 (mp0) outliers start: 52 outliers final: 27 residues processed: 175 average time/residue: 0.7764 time to fit residues: 150.9925 Evaluate side-chains 170 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 46 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.105350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.073014 restraints weight = 58402.100| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.21 r_work: 0.2942 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13276 Z= 0.211 Angle : 0.534 6.936 18040 Z= 0.283 Chirality : 0.039 0.165 2112 Planarity : 0.003 0.056 2222 Dihedral : 6.133 53.790 1882 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.06 % Allowed : 24.37 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.22), residues: 1672 helix: 2.27 (0.19), residues: 778 sheet: -0.61 (0.29), residues: 374 loop : -1.52 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 414 TYR 0.010 0.001 TYR C 86 PHE 0.025 0.001 PHE B 327 TRP 0.011 0.001 TRP B 98 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00479 (13268) covalent geometry : angle 0.53399 (18024) SS BOND : bond 0.00286 ( 8) SS BOND : angle 0.77415 ( 16) hydrogen bonds : bond 0.04532 ( 726) hydrogen bonds : angle 4.45915 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 137 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.7435 (mtm) REVERT: E 79 GLU cc_start: 0.7616 (mp0) cc_final: 0.6983 (mp0) REVERT: E 105 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: E 107 LYS cc_start: 0.8812 (tptt) cc_final: 0.8540 (tppp) REVERT: D 46 GLU cc_start: 0.8999 (tt0) cc_final: 0.8351 (tt0) REVERT: D 62 GLU cc_start: 0.8580 (mp0) cc_final: 0.8313 (mp0) REVERT: D 171 VAL cc_start: 0.9443 (OUTLIER) cc_final: 0.9230 (t) REVERT: D 182 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6099 (tm) REVERT: F 10 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7710 (mt-10) REVERT: F 13 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8365 (mttm) REVERT: F 62 GLU cc_start: 0.8579 (mp0) cc_final: 0.8280 (mp0) REVERT: F 108 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.6605 (mmt) REVERT: F 215 ASP cc_start: 0.7783 (m-30) cc_final: 0.7234 (t70) REVERT: C 4 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.7372 (mtm) REVERT: C 39 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8641 (mttm) REVERT: C 79 GLU cc_start: 0.7512 (mp0) cc_final: 0.6917 (mp0) REVERT: C 105 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7205 (tm-30) outliers start: 58 outliers final: 33 residues processed: 177 average time/residue: 0.7728 time to fit residues: 152.2211 Evaluate side-chains 178 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 4 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.105241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.073051 restraints weight = 57892.471| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.15 r_work: 0.2954 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13276 Z= 0.198 Angle : 0.526 5.710 18040 Z= 0.279 Chirality : 0.039 0.164 2112 Planarity : 0.003 0.055 2222 Dihedral : 6.073 54.242 1882 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.06 % Allowed : 24.44 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.22), residues: 1672 helix: 2.26 (0.19), residues: 780 sheet: -0.64 (0.29), residues: 374 loop : -1.54 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 414 TYR 0.009 0.001 TYR E 86 PHE 0.024 0.001 PHE B 327 TRP 0.011 0.001 TRP B 98 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00449 (13268) covalent geometry : angle 0.52600 (18024) SS BOND : bond 0.00173 ( 8) SS BOND : angle 0.72818 ( 16) hydrogen bonds : bond 0.04471 ( 726) hydrogen bonds : angle 4.41699 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 134 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.7438 (mtm) REVERT: E 79 GLU cc_start: 0.7612 (mp0) cc_final: 0.7081 (mp0) REVERT: E 105 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: E 107 LYS cc_start: 0.8809 (tptt) cc_final: 0.8542 (tppp) REVERT: D 62 GLU cc_start: 0.8562 (mp0) cc_final: 0.8291 (mp0) REVERT: D 171 VAL cc_start: 0.9451 (OUTLIER) cc_final: 0.9245 (t) REVERT: D 182 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6109 (tm) REVERT: D 216 LYS cc_start: 0.7413 (tptt) cc_final: 0.7086 (tppt) REVERT: F 10 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7692 (mt-10) REVERT: F 13 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8381 (mttm) REVERT: F 62 GLU cc_start: 0.8574 (mp0) cc_final: 0.8270 (mp0) REVERT: F 108 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.6710 (mmt) REVERT: F 215 ASP cc_start: 0.7808 (m-30) cc_final: 0.7255 (t70) REVERT: C 4 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.7360 (mtm) REVERT: C 79 GLU cc_start: 0.7510 (mp0) cc_final: 0.6908 (mp0) REVERT: C 105 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7201 (tm-30) outliers start: 58 outliers final: 32 residues processed: 179 average time/residue: 0.7777 time to fit residues: 154.9761 Evaluate side-chains 173 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 38 optimal weight: 20.0000 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.104919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.072672 restraints weight = 58478.499| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.17 r_work: 0.2955 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13276 Z= 0.212 Angle : 0.541 6.865 18040 Z= 0.286 Chirality : 0.039 0.168 2112 Planarity : 0.004 0.060 2222 Dihedral : 6.029 55.060 1882 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.43 % Allowed : 25.49 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.22), residues: 1672 helix: 2.25 (0.19), residues: 780 sheet: -0.66 (0.29), residues: 374 loop : -1.54 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 414 TYR 0.010 0.001 TYR D 50 PHE 0.026 0.001 PHE B 327 TRP 0.011 0.001 TRP B 98 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00482 (13268) covalent geometry : angle 0.54120 (18024) SS BOND : bond 0.00188 ( 8) SS BOND : angle 0.75837 ( 16) hydrogen bonds : bond 0.04520 ( 726) hydrogen bonds : angle 4.41502 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.7455 (mtm) REVERT: E 79 GLU cc_start: 0.7606 (mp0) cc_final: 0.6961 (mp0) REVERT: E 105 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: E 107 LYS cc_start: 0.8783 (tptt) cc_final: 0.8516 (tppp) REVERT: D 46 GLU cc_start: 0.8978 (tt0) cc_final: 0.8395 (tt0) REVERT: D 62 GLU cc_start: 0.8552 (mp0) cc_final: 0.8276 (mp0) REVERT: D 171 VAL cc_start: 0.9439 (OUTLIER) cc_final: 0.9230 (t) REVERT: D 182 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.6119 (tm) REVERT: D 216 LYS cc_start: 0.7453 (tptt) cc_final: 0.7172 (ttmt) REVERT: F 10 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7675 (mt-10) REVERT: F 13 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8382 (mttm) REVERT: F 62 GLU cc_start: 0.8589 (mp0) cc_final: 0.8279 (mp0) REVERT: F 108 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.6668 (mmt) REVERT: F 215 ASP cc_start: 0.7803 (m-30) cc_final: 0.7247 (t70) REVERT: C 4 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.7361 (mtm) REVERT: C 39 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8654 (mttm) REVERT: C 79 GLU cc_start: 0.7543 (mp0) cc_final: 0.6857 (mp0) REVERT: C 105 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7187 (tm-30) outliers start: 49 outliers final: 33 residues processed: 169 average time/residue: 0.8162 time to fit residues: 152.8775 Evaluate side-chains 171 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 122 optimal weight: 3.9990 chunk 62 optimal weight: 0.0270 chunk 30 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.106312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.074123 restraints weight = 57760.958| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.17 r_work: 0.2963 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13276 Z= 0.124 Angle : 0.506 7.369 18040 Z= 0.265 Chirality : 0.037 0.147 2112 Planarity : 0.004 0.068 2222 Dihedral : 5.859 54.434 1882 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 25.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.38 % Allowed : 26.68 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.22), residues: 1672 helix: 2.41 (0.19), residues: 780 sheet: -0.51 (0.29), residues: 368 loop : -1.48 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 414 TYR 0.009 0.001 TYR B 225 PHE 0.018 0.001 PHE B 327 TRP 0.012 0.001 TRP A 98 HIS 0.002 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00277 (13268) covalent geometry : angle 0.50569 (18024) SS BOND : bond 0.00139 ( 8) SS BOND : angle 0.63446 ( 16) hydrogen bonds : bond 0.04143 ( 726) hydrogen bonds : angle 4.25871 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.7408 (mtm) REVERT: E 79 GLU cc_start: 0.7543 (mp0) cc_final: 0.6940 (mp0) REVERT: E 105 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: E 107 LYS cc_start: 0.8782 (tptt) cc_final: 0.8521 (tppp) REVERT: E 188 ARG cc_start: 0.8879 (ptp-110) cc_final: 0.8163 (ptp-110) REVERT: D 46 GLU cc_start: 0.8937 (tt0) cc_final: 0.8365 (tt0) REVERT: D 62 GLU cc_start: 0.8548 (mp0) cc_final: 0.8270 (mp0) REVERT: D 182 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6112 (tm) REVERT: F 10 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7616 (mt-10) REVERT: F 13 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8366 (mttm) REVERT: F 62 GLU cc_start: 0.8597 (mp0) cc_final: 0.8288 (mp0) REVERT: F 108 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.6393 (mmt) REVERT: F 215 ASP cc_start: 0.7874 (m-30) cc_final: 0.7310 (t70) REVERT: C 4 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.7342 (mtm) REVERT: C 39 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8635 (mttm) REVERT: C 79 GLU cc_start: 0.7461 (mp0) cc_final: 0.6858 (mp0) REVERT: C 105 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: C 185 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7948 (mm-30) outliers start: 34 outliers final: 21 residues processed: 162 average time/residue: 0.8552 time to fit residues: 153.1396 Evaluate side-chains 163 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 150 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.073647 restraints weight = 57908.352| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.17 r_work: 0.2954 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13276 Z= 0.173 Angle : 0.522 7.554 18040 Z= 0.274 Chirality : 0.038 0.148 2112 Planarity : 0.004 0.071 2222 Dihedral : 5.841 55.820 1882 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.52 % Allowed : 26.54 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.22), residues: 1672 helix: 2.42 (0.19), residues: 780 sheet: -0.46 (0.29), residues: 368 loop : -1.49 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 414 TYR 0.009 0.001 TYR B 225 PHE 0.021 0.001 PHE B 327 TRP 0.011 0.001 TRP A 98 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00392 (13268) covalent geometry : angle 0.52196 (18024) SS BOND : bond 0.00164 ( 8) SS BOND : angle 0.70907 ( 16) hydrogen bonds : bond 0.04218 ( 726) hydrogen bonds : angle 4.26146 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.7474 (mtm) REVERT: E 79 GLU cc_start: 0.7520 (mp0) cc_final: 0.6982 (mp0) REVERT: E 105 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: E 107 LYS cc_start: 0.8769 (tptt) cc_final: 0.8508 (tppp) REVERT: D 46 GLU cc_start: 0.8940 (tt0) cc_final: 0.8312 (tt0) REVERT: D 62 GLU cc_start: 0.8573 (mp0) cc_final: 0.8286 (mp0) REVERT: D 182 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6047 (tm) REVERT: F 10 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7618 (mt-10) REVERT: F 62 GLU cc_start: 0.8601 (mp0) cc_final: 0.8278 (mp0) REVERT: F 108 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.6543 (mmt) REVERT: F 215 ASP cc_start: 0.7875 (m-30) cc_final: 0.7320 (t70) REVERT: C 4 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.7334 (mtm) REVERT: C 39 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8620 (mttm) REVERT: C 79 GLU cc_start: 0.7452 (mp0) cc_final: 0.6850 (mp0) REVERT: C 105 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7152 (tm-30) outliers start: 36 outliers final: 22 residues processed: 160 average time/residue: 0.8347 time to fit residues: 147.5005 Evaluate side-chains 160 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 150 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 127 optimal weight: 0.2980 chunk 54 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.107080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.075054 restraints weight = 57677.587| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.17 r_work: 0.2984 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13276 Z= 0.122 Angle : 0.505 7.514 18040 Z= 0.262 Chirality : 0.037 0.143 2112 Planarity : 0.004 0.072 2222 Dihedral : 5.678 56.353 1882 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.82 % Allowed : 27.31 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.04 (0.22), residues: 1672 helix: 2.56 (0.19), residues: 780 sheet: -0.42 (0.29), residues: 368 loop : -1.42 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 414 TYR 0.008 0.001 TYR C 186 PHE 0.016 0.001 PHE B 327 TRP 0.011 0.001 TRP A 98 HIS 0.002 0.000 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00274 (13268) covalent geometry : angle 0.50532 (18024) SS BOND : bond 0.00147 ( 8) SS BOND : angle 0.62390 ( 16) hydrogen bonds : bond 0.03894 ( 726) hydrogen bonds : angle 4.12459 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.7342 (mtm) REVERT: E 5 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8749 (p) REVERT: E 79 GLU cc_start: 0.7562 (mp0) cc_final: 0.6931 (mp0) REVERT: E 105 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: E 107 LYS cc_start: 0.8777 (tptt) cc_final: 0.8490 (tppp) REVERT: D 46 GLU cc_start: 0.8917 (tt0) cc_final: 0.8341 (tt0) REVERT: D 62 GLU cc_start: 0.8531 (mp0) cc_final: 0.8260 (mp0) REVERT: D 216 LYS cc_start: 0.7444 (tptt) cc_final: 0.7122 (tppt) REVERT: F 10 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7601 (mt-10) REVERT: F 62 GLU cc_start: 0.8581 (mp0) cc_final: 0.8267 (mp0) REVERT: F 108 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.6224 (mmt) REVERT: F 215 ASP cc_start: 0.7946 (m-30) cc_final: 0.7405 (t70) REVERT: C 4 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.7353 (mtm) REVERT: C 39 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8622 (mttm) REVERT: C 79 GLU cc_start: 0.7486 (mp0) cc_final: 0.6900 (mp0) REVERT: C 105 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: C 107 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8927 (tppp) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 0.8566 time to fit residues: 139.7399 Evaluate side-chains 148 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 142 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 54 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN D 5 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.107346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.075655 restraints weight = 58959.041| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.20 r_work: 0.2976 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13276 Z= 0.141 Angle : 0.534 14.514 18040 Z= 0.277 Chirality : 0.038 0.260 2112 Planarity : 0.004 0.114 2222 Dihedral : 5.658 57.705 1882 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.96 % Allowed : 27.38 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.06 (0.22), residues: 1672 helix: 2.59 (0.19), residues: 778 sheet: -0.37 (0.29), residues: 368 loop : -1.43 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 414 TYR 0.010 0.001 TYR C 186 PHE 0.017 0.001 PHE B 327 TRP 0.011 0.001 TRP A 98 HIS 0.002 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00321 (13268) covalent geometry : angle 0.53382 (18024) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.63667 ( 16) hydrogen bonds : bond 0.03908 ( 726) hydrogen bonds : angle 4.10680 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5420.43 seconds wall clock time: 93 minutes 9.46 seconds (5589.46 seconds total)