Starting phenix.real_space_refine on Thu Jul 2 09:35:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hpt_34943/07_2026/8hpt_34943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpt_34943/07_2026/8hpt_34943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hpt_34943/07_2026/8hpt_34943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpt_34943/07_2026/8hpt_34943.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hpt_34943/07_2026/8hpt_34943.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hpt_34943/07_2026/8hpt_34943.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hpt_34943/07_2026/8hpt_34943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpt_34943/07_2026/8hpt_34943.map" } resolution = 3.39 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= 0.024 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5051 2.51 5 N 1343 2.21 5 O 1455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7897 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1872 Classifications: {'peptide': 255} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 50 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MEA:plan-2': 1, 'ZAL:plan-1': 1, 'ALC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1458 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 48} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2436 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 7, 'ASP:plan': 8, 'ASN:plan1': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 395 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1674 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 1.92, per 1000 atoms: 0.24 Number of scatterers: 7897 At special positions: 0 Unit cell: (89.0706, 126.025, 128.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1455 8.00 N 1343 7.00 C 5051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 501.7 milliseconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB ZAL D 404 " Input residue name is d-peptide pdb=" CB DAR D 406 " Number of C-beta restraints generated: 2032 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 38.2% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 36 through 63 removed outlier: 3.599A pdb=" N ALA A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 64 through 65 No H-bonds generated for 'chain 'A' and resid 64 through 65' Processing helix chain 'A' and resid 69 through 69 No H-bonds generated for 'chain 'A' and resid 69 through 69' Processing helix chain 'A' and resid 70 through 87 removed outlier: 4.360A pdb=" N TRP A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.514A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.792A pdb=" N CYS A 109 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 110 " --> pdb=" O THR A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 106 through 110' Processing helix chain 'A' and resid 111 through 140 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.537A pdb=" N VAL A 147 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 202 through 231 removed outlier: 5.591A pdb=" N LEU A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 232 through 237 removed outlier: 6.955A pdb=" N ALA A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 237 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 266 removed outlier: 3.572A pdb=" N LYS A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 276 through 305 removed outlier: 3.668A pdb=" N GLU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Proline residue: A 298 - end of helix removed outlier: 3.970A pdb=" N TYR A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.783A pdb=" N HIS A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 31 removed outlier: 3.906A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.917A pdb=" N TRP B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.660A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.933A pdb=" N ALA B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.562A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.979A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.709A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.903A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.021A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.930A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 191 removed outlier: 7.315A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.578A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.118A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.235A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.956A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.569A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.589A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.554A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 277 removed outlier: 4.019A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.592A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.550A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.523A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1098 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: 0.94 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1277 1.32 - 1.44: 2222 1.44 - 1.56: 4498 1.56 - 1.69: 1 1.69 - 1.81: 65 Bond restraints: 8063 Sorted by residual: bond pdb=" C PRO A 298 " pdb=" O PRO A 298 " ideal model delta sigma weight residual 1.234 1.193 0.041 1.00e-02 1.00e+04 1.72e+01 bond pdb=" N LEU A 276 " pdb=" CA LEU A 276 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" C PRO A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 1.333 1.361 -0.028 1.01e-02 9.80e+03 7.45e+00 bond pdb=" C PRO A 170 " pdb=" O PRO A 170 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.26e-02 6.30e+03 6.57e+00 bond pdb=" N ASP H 223 " pdb=" CA ASP H 223 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.33e-02 5.65e+03 5.81e+00 ... (remaining 8058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 10821 1.93 - 3.86: 149 3.86 - 5.80: 32 5.80 - 7.73: 4 7.73 - 9.66: 2 Bond angle restraints: 11008 Sorted by residual: angle pdb=" N PRO A 170 " pdb=" CA PRO A 170 " pdb=" C PRO A 170 " ideal model delta sigma weight residual 113.53 108.21 5.32 1.39e+00 5.18e-01 1.47e+01 angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.53 109.85 3.68 9.80e-01 1.04e+00 1.41e+01 angle pdb=" O ILE A 169 " pdb=" C ILE A 169 " pdb=" N PRO A 170 " ideal model delta sigma weight residual 121.10 117.10 4.00 1.14e+00 7.69e-01 1.23e+01 angle pdb=" CB MET H 83 " pdb=" CG MET H 83 " pdb=" SD MET H 83 " ideal model delta sigma weight residual 112.70 122.36 -9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CA ASP H 223 " pdb=" CB ASP H 223 " pdb=" CG ASP H 223 " ideal model delta sigma weight residual 112.60 115.78 -3.18 1.00e+00 1.00e+00 1.01e+01 ... (remaining 11003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 4363 23.48 - 46.96: 281 46.96 - 70.43: 21 70.43 - 93.91: 5 93.91 - 117.39: 1 Dihedral angle restraints: 4671 sinusoidal: 1522 harmonic: 3149 Sorted by residual: dihedral pdb=" CA GLY A 51 " pdb=" C GLY A 51 " pdb=" N VAL A 52 " pdb=" CA VAL A 52 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CG ALC D 405 " pdb=" CD1 ALC D 405 " pdb=" CE1 ALC D 405 " pdb=" CZ ALC D 405 " ideal model delta sinusoidal sigma weight residual -55.84 61.55 -117.39 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" CA LEU A 269 " pdb=" C LEU A 269 " pdb=" N PRO A 270 " pdb=" CA PRO A 270 " ideal model delta harmonic sigma weight residual -180.00 -160.28 -19.72 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1028 0.047 - 0.095: 219 0.095 - 0.142: 56 0.142 - 0.190: 2 0.190 - 0.237: 2 Chirality restraints: 1307 Sorted by residual: chirality pdb=" CB ILE A 169 " pdb=" CA ILE A 169 " pdb=" CG1 ILE A 169 " pdb=" CG2 ILE A 169 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA DAR D 406 " pdb=" N DAR D 406 " pdb=" C DAR D 406 " pdb=" CB DAR D 406 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 266 " pdb=" CA ILE A 266 " pdb=" CG1 ILE A 266 " pdb=" CG2 ILE A 266 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1304 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD DAR D 406 " 0.250 2.00e-02 2.50e+03 2.13e-01 5.67e+02 pdb=" NE DAR D 406 " -0.356 2.00e-02 2.50e+03 pdb=" CZ DAR D 406 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 DAR D 406 " 0.183 2.00e-02 2.50e+03 pdb=" NH2 DAR D 406 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO H 14 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 74 " 0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO H 75 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO H 75 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 75 " 0.047 5.00e-02 4.00e+02 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 839 2.75 - 3.29: 7623 3.29 - 3.82: 12777 3.82 - 4.36: 13850 4.36 - 4.90: 25606 Nonbonded interactions: 60695 Sorted by model distance: nonbonded pdb=" O ARG H 67 " pdb=" OG1 THR H 84 " model vdw 2.212 3.040 nonbonded pdb=" O SER B 310 " pdb=" OG SER B 310 " model vdw 2.226 3.040 nonbonded pdb=" NH1 ARG H 180 " pdb=" O GLU H 222 " model vdw 2.306 3.120 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.325 3.040 nonbonded pdb=" OG1 THR C 128 " pdb=" O ASN C 132 " model vdw 2.351 3.040 ... (remaining 60690 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.003 0.095 8066 Z= 0.184 Angle : 0.595 9.662 11012 Z= 0.315 Chirality : 0.042 0.237 1307 Planarity : 0.008 0.213 1397 Dihedral : 14.625 117.389 2633 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.40 % Allowed : 8.30 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.29 (0.27), residues: 1067 helix: 1.87 (0.28), residues: 364 sheet: -0.21 (0.32), residues: 291 loop : -1.00 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 148 TYR 0.017 0.001 TYR B 297 PHE 0.025 0.001 PHE H 68 TRP 0.031 0.001 TRP A 268 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 ( 8063) covalent geometry : angle 0.59480 / 0.31 (11008) SS BOND : bond 0.00332 / 0.21 ( 2) SS BOND : angle 1.14157 / 0.60 ( 4) hydrogen bonds : bond 0.15889 / 10.65 ( 391) hydrogen bonds : angle 6.27360 / 4.69 ( 1098) Misc. bond : bond 0.09454 / 5.91 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.319 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 96 average time/residue: 0.0912 time to fit residues: 11.8599 Evaluate side-chains 93 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0670 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0980 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 0.7980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.177891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150219 restraints weight = 10402.767| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.82 r_work: 0.3589 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8066 Z= 0.110 Angle : 0.542 7.433 11012 Z= 0.279 Chirality : 0.041 0.191 1307 Planarity : 0.004 0.058 1397 Dihedral : 4.923 87.532 1166 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.07 % Allowed : 12.58 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.54 (0.27), residues: 1067 helix: 2.15 (0.29), residues: 364 sheet: -0.02 (0.32), residues: 290 loop : -0.97 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.015 0.001 TYR H 190 PHE 0.017 0.001 PHE H 68 TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8063) covalent geometry : angle 0.54219 / 0.28 (11008) SS BOND : bond 0.00366 / 0.21 ( 2) SS BOND : angle 0.91136 / 0.52 ( 4) hydrogen bonds : bond 0.03573 / 2.46 ( 391) hydrogen bonds : angle 4.70456 / 3.52 ( 1098) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.313 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 106 average time/residue: 0.0732 time to fit residues: 11.0239 Evaluate side-chains 104 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 79 optimal weight: 0.0470 chunk 63 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.174703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147318 restraints weight = 10343.122| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.72 r_work: 0.3556 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8066 Z= 0.128 Angle : 0.557 8.170 11012 Z= 0.284 Chirality : 0.042 0.185 1307 Planarity : 0.004 0.052 1397 Dihedral : 5.021 82.627 1166 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.87 % Allowed : 15.26 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.59 (0.27), residues: 1067 helix: 2.14 (0.28), residues: 365 sheet: 0.18 (0.32), residues: 295 loop : -1.06 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 18 TYR 0.016 0.001 TYR H 190 PHE 0.019 0.001 PHE H 68 TRP 0.007 0.001 TRP C 99 HIS 0.004 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8063) covalent geometry : angle 0.55686 / 0.28 (11008) SS BOND : bond 0.00514 / 0.30 ( 2) SS BOND : angle 1.08398 / 0.57 ( 4) hydrogen bonds : bond 0.03482 / 2.41 ( 391) hydrogen bonds : angle 4.43732 / 3.33 ( 1098) Misc. bond : bond 0.00025 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.291 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 115 average time/residue: 0.0831 time to fit residues: 13.3674 Evaluate side-chains 113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.173029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144714 restraints weight = 10474.289| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.76 r_work: 0.3503 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8066 Z= 0.141 Angle : 0.550 7.356 11012 Z= 0.283 Chirality : 0.042 0.157 1307 Planarity : 0.004 0.046 1397 Dihedral : 4.832 83.292 1165 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.08 % Allowed : 16.06 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.57 (0.27), residues: 1067 helix: 2.14 (0.28), residues: 364 sheet: 0.15 (0.32), residues: 300 loop : -1.08 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 18 TYR 0.015 0.001 TYR H 190 PHE 0.033 0.001 PHE H 68 TRP 0.007 0.001 TRP C 169 HIS 0.004 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8063) covalent geometry : angle 0.54990 / 0.28 (11008) SS BOND : bond 0.00501 / 0.29 ( 2) SS BOND : angle 0.92934 / 0.51 ( 4) hydrogen bonds : bond 0.03423 / 2.37 ( 391) hydrogen bonds : angle 4.42525 / 3.33 ( 1098) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.191 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 116 average time/residue: 0.0720 time to fit residues: 11.5330 Evaluate side-chains 121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 96 optimal weight: 4.9990 chunk 42 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.0040 chunk 83 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 ASN ** C 32 GLN ** 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 = 0.3998 r_free = 0.3998 target = 0.170447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142888 restraints weight = 10170.088| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.78 r_work: 0.3551 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8066 Z= 0.115 Angle : 0.526 7.237 11012 Z= 0.268 Chirality : 0.041 0.168 1307 Planarity : 0.004 0.044 1397 Dihedral : 4.723 81.447 1165 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.95 % Allowed : 17.54 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.63 (0.27), residues: 1067 helix: 2.20 (0.28), residues: 363 sheet: 0.21 (0.32), residues: 294 loop : -1.06 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 18 TYR 0.014 0.001 TYR H 190 PHE 0.028 0.001 PHE H 68 TRP 0.007 0.001 TRP C 169 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8063) covalent geometry : angle 0.52548 / 0.27 (11008) SS BOND : bond 0.00431 / 0.25 ( 2) SS BOND : angle 0.75690 / 0.40 ( 4) hydrogen bonds : bond 0.03158 / 2.20 ( 391) hydrogen bonds : angle 4.28710 / 3.23 ( 1098) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.280 Fit side-chains outliers start: 22 outliers final: 20 residues processed: 114 average time/residue: 0.0773 time to fit residues: 12.2348 Evaluate side-chains 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142831 restraints weight = 10262.484| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.76 r_work: 0.3516 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8066 Z= 0.132 Angle : 0.538 7.257 11012 Z= 0.276 Chirality : 0.042 0.172 1307 Planarity : 0.004 0.042 1397 Dihedral : 4.749 81.777 1165 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.48 % Allowed : 18.88 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.63 (0.27), residues: 1067 helix: 2.14 (0.28), residues: 366 sheet: 0.17 (0.32), residues: 303 loop : -1.00 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 18 TYR 0.017 0.001 TYR B 297 PHE 0.034 0.001 PHE H 68 TRP 0.006 0.001 TRP C 63 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8063) covalent geometry : angle 0.53791 / 0.28 (11008) SS BOND : bond 0.00485 / 0.28 ( 2) SS BOND : angle 0.86792 / 0.47 ( 4) hydrogen bonds : bond 0.03278 / 2.28 ( 391) hydrogen bonds : angle 4.31144 / 3.25 ( 1098) Misc. bond : bond 0.00008 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.204 Fit side-chains outliers start: 26 outliers final: 24 residues processed: 115 average time/residue: 0.0652 time to fit residues: 10.4443 Evaluate side-chains 124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.0010 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.174494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.146250 restraints weight = 10488.196| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.76 r_work: 0.3537 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8066 Z= 0.106 Angle : 0.513 7.246 11012 Z= 0.262 Chirality : 0.041 0.193 1307 Planarity : 0.004 0.040 1397 Dihedral : 4.643 80.174 1165 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.95 % Allowed : 20.08 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.72 (0.27), residues: 1067 helix: 2.24 (0.28), residues: 365 sheet: 0.20 (0.32), residues: 296 loop : -0.94 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 18 TYR 0.013 0.001 TYR H 190 PHE 0.028 0.001 PHE H 68 TRP 0.007 0.001 TRP C 63 HIS 0.002 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8063) covalent geometry : angle 0.51340 / 0.26 (11008) SS BOND : bond 0.00386 / 0.23 ( 2) SS BOND : angle 0.65526 / 0.34 ( 4) hydrogen bonds : bond 0.02991 / 2.08 ( 391) hydrogen bonds : angle 4.19054 / 3.15 ( 1098) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.271 Fit side-chains REVERT: A 238 SER cc_start: 0.8148 (t) cc_final: 0.7708 (p) outliers start: 22 outliers final: 20 residues processed: 110 average time/residue: 0.0696 time to fit residues: 10.6301 Evaluate side-chains 118 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 0.0370 chunk 51 optimal weight: 0.2980 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135719 restraints weight = 9960.010| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.44 r_work: 0.3425 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8066 Z= 0.117 Angle : 0.535 7.252 11012 Z= 0.271 Chirality : 0.041 0.189 1307 Planarity : 0.004 0.039 1397 Dihedral : 4.650 80.441 1165 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.75 % Allowed : 19.68 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.71 (0.27), residues: 1067 helix: 2.24 (0.28), residues: 361 sheet: 0.14 (0.32), residues: 295 loop : -0.87 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 18 TYR 0.014 0.001 TYR H 190 PHE 0.032 0.001 PHE H 68 TRP 0.007 0.001 TRP C 63 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8063) covalent geometry : angle 0.53499 / 0.27 (11008) SS BOND : bond 0.00423 / 0.25 ( 2) SS BOND : angle 0.73936 / 0.40 ( 4) hydrogen bonds : bond 0.03081 / 2.14 ( 391) hydrogen bonds : angle 4.19097 / 3.16 ( 1098) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.227 Fit side-chains REVERT: A 265 MET cc_start: 0.8297 (tpp) cc_final: 0.8048 (tpp) outliers start: 28 outliers final: 24 residues processed: 114 average time/residue: 0.0699 time to fit residues: 11.1860 Evaluate side-chains 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134627 restraints weight = 9988.966| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.46 r_work: 0.3411 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8066 Z= 0.133 Angle : 0.551 7.254 11012 Z= 0.280 Chirality : 0.042 0.196 1307 Planarity : 0.004 0.040 1397 Dihedral : 4.725 81.403 1165 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.61 % Allowed : 19.68 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.27), residues: 1067 helix: 2.20 (0.28), residues: 361 sheet: 0.13 (0.32), residues: 297 loop : -0.88 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 18 TYR 0.014 0.001 TYR H 190 PHE 0.034 0.001 PHE H 68 TRP 0.005 0.001 TRP A 256 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 8063) covalent geometry : angle 0.55114 / 0.28 (11008) SS BOND : bond 0.00453 / 0.26 ( 2) SS BOND : angle 0.81296 / 0.45 ( 4) hydrogen bonds : bond 0.03206 / 2.22 ( 391) hydrogen bonds : angle 4.26294 / 3.22 ( 1098) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.296 Fit side-chains REVERT: A 265 MET cc_start: 0.8329 (tpp) cc_final: 0.8081 (tpp) outliers start: 27 outliers final: 26 residues processed: 111 average time/residue: 0.0838 time to fit residues: 13.1169 Evaluate side-chains 119 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.0050 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.161345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135958 restraints weight = 9911.527| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.48 r_work: 0.3423 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8066 Z= 0.116 Angle : 0.544 8.280 11012 Z= 0.276 Chirality : 0.042 0.189 1307 Planarity : 0.004 0.043 1397 Dihedral : 4.692 80.769 1165 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.48 % Allowed : 20.21 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.27), residues: 1067 helix: 2.19 (0.28), residues: 361 sheet: 0.18 (0.33), residues: 290 loop : -0.86 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 18 TYR 0.013 0.001 TYR H 190 PHE 0.032 0.001 PHE H 68 TRP 0.010 0.001 TRP A 154 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8063) covalent geometry : angle 0.54393 / 0.28 (11008) SS BOND : bond 0.00414 / 0.24 ( 2) SS BOND : angle 0.72242 / 0.39 ( 4) hydrogen bonds : bond 0.03100 / 2.16 ( 391) hydrogen bonds : angle 4.23774 / 3.20 ( 1098) Misc. bond : bond 0.00004 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.267 Fit side-chains REVERT: A 265 MET cc_start: 0.8326 (tpp) cc_final: 0.8092 (tpp) REVERT: H 18 ARG cc_start: 0.6817 (tpp80) cc_final: 0.6583 (ttm-80) outliers start: 26 outliers final: 25 residues processed: 109 average time/residue: 0.0693 time to fit residues: 10.7583 Evaluate side-chains 119 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.162793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.136747 restraints weight = 9870.647| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.37 r_work: 0.3427 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8066 Z= 0.103 Angle : 0.530 8.510 11012 Z= 0.267 Chirality : 0.041 0.186 1307 Planarity : 0.004 0.042 1397 Dihedral : 4.595 79.277 1165 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.35 % Allowed : 20.48 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.77 (0.27), residues: 1067 helix: 2.22 (0.28), residues: 364 sheet: 0.29 (0.32), residues: 294 loop : -0.88 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 18 TYR 0.013 0.001 TYR H 190 PHE 0.029 0.001 PHE H 68 TRP 0.007 0.001 TRP C 169 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 8063) covalent geometry : angle 0.52950 / 0.27 (11008) SS BOND : bond 0.00371 / 0.22 ( 2) SS BOND : angle 0.64966 / 0.34 ( 4) hydrogen bonds : bond 0.02905 / 2.02 ( 391) hydrogen bonds : angle 4.16884 / 3.14 ( 1098) Misc. bond : bond 0.00000 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1945.77 seconds wall clock time: 33 minutes 59.22 seconds (2039.22 seconds total)