Starting phenix.real_space_refine on Fri Aug 22 21:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpt_34943/08_2025/8hpt_34943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpt_34943/08_2025/8hpt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpt_34943/08_2025/8hpt_34943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpt_34943/08_2025/8hpt_34943.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpt_34943/08_2025/8hpt_34943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpt_34943/08_2025/8hpt_34943.cif" } 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-2.0-5787/lib/python3.9/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} Modifications used: {'COO': 1, 'PEPT-D': 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: 2.31, per 1000 atoms: 0.29 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: 0.82 Conformation dependent library (CDL) restraints added in 469.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.30 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: 1.30 Time building geometry restraints manager: 0.99 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: 10823 1.93 - 3.86: 147 3.86 - 5.80: 31 5.80 - 7.73: 4 7.73 - 9.66: 3 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 - 26.57: 4426 26.57 - 53.13: 229 53.13 - 79.70: 15 79.70 - 106.27: 2 106.27 - 132.83: 2 Dihedral angle restraints: 4674 sinusoidal: 1525 harmonic: 3149 Sorted by residual: dihedral pdb=" CD DAR D 406 " pdb=" NE DAR D 406 " pdb=" CZ DAR D 406 " pdb=" NH1 DAR D 406 " ideal model delta sinusoidal sigma weight residual 0.00 -132.83 132.83 1 1.00e+01 1.00e-02 1.61e+02 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 ... (remaining 4671 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 -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.10e+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 " 0.801 9.50e-02 1.11e+02 3.59e-01 7.84e+01 pdb=" NE DAR D 406 " -0.047 2.00e-02 2.50e+03 pdb=" CZ DAR D 406 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 DAR D 406 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 DAR D 406 " -0.002 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.280 Find NCS groups from input model: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.598 9.662 11012 Z= 0.315 Chirality : 0.042 0.237 1307 Planarity : 0.011 0.359 1397 Dihedral : 14.892 132.831 2636 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 aren 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 covalent geometry : bond 0.00275 ( 8063) covalent geometry : angle 0.59741 (11008) SS BOND : bond 0.00332 ( 2) SS BOND : angle 1.14157 ( 4) hydrogen bonds : bond 0.15889 ( 391) hydrogen bonds : angle 6.27360 ( 1098) Misc. bond : bond 0.09454 ( 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 : 0.304 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 96 average time/residue: 0.0969 time to fit residues: 12.6054 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 : 0.268 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.177958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150409 restraints weight = 10391.629| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.80 r_work: 0.3593 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0889 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= 0.109 Angle : 0.540 7.523 11012 Z= 0.277 Chirality : 0.041 0.173 1307 Planarity : 0.005 0.058 1397 Dihedral : 7.161 173.262 1169 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.07 % Allowed : 12.72 % Favored : 86.21 % 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 aren not related in a simple way. whole: 0.55 (0.27), residues: 1067 helix: 2.16 (0.29), residues: 364 sheet: 0.04 (0.32), residues: 296 loop : -1.02 (0.30), residues: 407 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 0.018 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 covalent geometry : bond 0.00234 ( 8063) covalent geometry : angle 0.53986 (11008) SS BOND : bond 0.00382 ( 2) SS BOND : angle 0.96986 ( 4) hydrogen bonds : bond 0.03442 ( 391) hydrogen bonds : angle 4.64412 ( 1098) Misc. bond : bond 0.00048 ( 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 : 0.189 Fit side-chains REVERT: H 91 THR cc_start: 0.8404 (t) cc_final: 0.8200 (t) outliers start: 8 outliers final: 6 residues processed: 105 average time/residue: 0.0804 time to fit residues: 11.5156 Evaluate side-chains 103 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 H residue 109 ASP 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: 0.9980 chunk 69 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4004 r_free = 0.4004 target = 0.172951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144795 restraints weight = 10328.515| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.77 r_work: 0.3519 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8066 Z= 0.150 Angle : 0.567 7.450 11012 Z= 0.292 Chirality : 0.042 0.167 1307 Planarity : 0.004 0.054 1397 Dihedral : 7.375 178.586 1169 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.14 % Allowed : 15.39 % Favored : 82.46 % 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 aren not related in a simple way. whole: 0.53 (0.27), residues: 1067 helix: 2.10 (0.29), residues: 364 sheet: 0.07 (0.31), residues: 302 loop : -1.05 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.016 0.001 TYR H 190 PHE 0.031 0.002 PHE H 68 TRP 0.007 0.001 TRP C 99 HIS 0.005 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8063) covalent geometry : angle 0.56703 (11008) SS BOND : bond 0.00534 ( 2) SS BOND : angle 1.14771 ( 4) hydrogen bonds : bond 0.03710 ( 391) hydrogen bonds : angle 4.50242 ( 1098) Misc. bond : bond 0.00006 ( 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 125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.297 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 118 average time/residue: 0.0910 time to fit residues: 14.6126 Evaluate side-chains 114 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU 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 273 ASP Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 71 VAL 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 172 THR 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: 1.9990 chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 60 optimal weight: 0.3980 chunk 70 optimal weight: 0.0770 chunk 13 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4017 r_free = 0.4017 target = 0.174009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145462 restraints weight = 10452.218| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.81 r_work: 0.3538 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1547 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= 0.119 Angle : 0.527 7.183 11012 Z= 0.271 Chirality : 0.041 0.170 1307 Planarity : 0.004 0.047 1397 Dihedral : 7.099 179.363 1168 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.35 % Allowed : 16.60 % Favored : 80.05 % 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 aren not related in a simple way. whole: 0.60 (0.27), residues: 1067 helix: 2.18 (0.28), residues: 362 sheet: 0.16 (0.32), residues: 294 loop : -1.03 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 18 TYR 0.015 0.001 TYR B 297 PHE 0.027 0.001 PHE H 68 TRP 0.008 0.001 TRP C 169 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8063) covalent geometry : angle 0.52710 (11008) SS BOND : bond 0.00439 ( 2) SS BOND : angle 0.80684 ( 4) hydrogen bonds : bond 0.03267 ( 391) hydrogen bonds : angle 4.36441 ( 1098) Misc. bond : bond 0.00005 ( 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 134 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.312 Fit side-chains outliers start: 25 outliers final: 19 residues processed: 122 average time/residue: 0.0920 time to fit residues: 15.2355 Evaluate side-chains 124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 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 273 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.0370 chunk 83 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4017 r_free = 0.4017 target = 0.173967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145718 restraints weight = 10496.884| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.75 r_work: 0.3534 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1696 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 : 0.519 7.254 11012 Z= 0.266 Chirality : 0.041 0.166 1307 Planarity : 0.004 0.045 1397 Dihedral : 7.019 179.187 1168 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.08 % Allowed : 18.07 % Favored : 78.85 % 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 aren not related in a simple way. whole: 0.67 (0.27), residues: 1067 helix: 2.21 (0.28), residues: 363 sheet: 0.21 (0.32), residues: 293 loop : -0.98 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 18 TYR 0.014 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 C 142 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8063) covalent geometry : angle 0.51911 (11008) SS BOND : bond 0.00438 ( 2) SS BOND : angle 0.77769 ( 4) hydrogen bonds : bond 0.03158 ( 391) hydrogen bonds : angle 4.27315 ( 1098) Misc. bond : bond 0.00007 ( 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 128 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.311 Fit side-chains REVERT: G 38 MET cc_start: 0.7852 (ttt) cc_final: 0.7529 (ttm) outliers start: 23 outliers final: 19 residues processed: 117 average time/residue: 0.0821 time to fit residues: 13.2378 Evaluate side-chains 121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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 273 ASP Chi-restraints excluded: chain B residue 310 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 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 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 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 = 0.3985 r_free = 0.3985 target = 0.170961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142469 restraints weight = 10401.046| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.76 r_work: 0.3491 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8066 Z= 0.156 Angle : 0.557 7.269 11012 Z= 0.286 Chirality : 0.042 0.173 1307 Planarity : 0.004 0.043 1397 Dihedral : 7.113 178.891 1168 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.61 % Allowed : 18.61 % Favored : 77.78 % 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 aren not related in a simple way. whole: 0.58 (0.27), residues: 1067 helix: 2.10 (0.28), residues: 365 sheet: 0.10 (0.31), residues: 304 loop : -1.00 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 18 TYR 0.016 0.001 TYR B 297 PHE 0.038 0.002 PHE H 68 TRP 0.008 0.001 TRP A 256 HIS 0.004 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8063) covalent geometry : angle 0.55642 (11008) SS BOND : bond 0.00521 ( 2) SS BOND : angle 0.95028 ( 4) hydrogen bonds : bond 0.03507 ( 391) hydrogen bonds : angle 4.40889 ( 1098) Misc. bond : bond 0.00011 ( 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 128 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.274 Fit side-chains REVERT: G 38 MET cc_start: 0.7783 (ttt) cc_final: 0.7541 (ttm) outliers start: 27 outliers final: 25 residues processed: 116 average time/residue: 0.0842 time to fit residues: 13.3330 Evaluate side-chains 125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 48 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.159369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133204 restraints weight = 10094.987| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.45 r_work: 0.3401 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8066 Z= 0.141 Angle : 0.540 7.263 11012 Z= 0.278 Chirality : 0.042 0.190 1307 Planarity : 0.004 0.041 1397 Dihedral : 7.080 179.064 1168 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.42 % Allowed : 18.61 % 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 aren not related in a simple way. whole: 0.56 (0.27), residues: 1067 helix: 2.08 (0.28), residues: 361 sheet: 0.08 (0.31), residues: 303 loop : -0.96 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 18 TYR 0.015 0.001 TYR H 190 PHE 0.035 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 covalent geometry : bond 0.00331 ( 8063) covalent geometry : angle 0.54037 (11008) SS BOND : bond 0.00477 ( 2) SS BOND : angle 0.82662 ( 4) hydrogen bonds : bond 0.03366 ( 391) hydrogen bonds : angle 4.38379 ( 1098) Misc. bond : bond 0.00013 ( 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 135 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.245 Fit side-chains REVERT: G 38 MET cc_start: 0.7777 (ttt) cc_final: 0.7557 (ttm) outliers start: 33 outliers final: 29 residues processed: 121 average time/residue: 0.0860 time to fit residues: 14.2865 Evaluate side-chains 127 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 273 ASP 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 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 84 THR Chi-restraints excluded: chain H residue 97 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 51 optimal weight: 0.1980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134282 restraints weight = 9962.464| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.41 r_work: 0.3421 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8066 Z= 0.128 Angle : 0.538 7.260 11012 Z= 0.276 Chirality : 0.042 0.224 1307 Planarity : 0.004 0.041 1397 Dihedral : 7.038 179.293 1168 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.42 % Allowed : 18.88 % 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 aren not related in a simple way. whole: 0.60 (0.27), residues: 1067 helix: 2.14 (0.28), residues: 361 sheet: 0.05 (0.31), residues: 305 loop : -0.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 18 TYR 0.018 0.001 TYR B 297 PHE 0.035 0.001 PHE H 68 TRP 0.008 0.001 TRP C 63 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8063) covalent geometry : angle 0.53767 (11008) SS BOND : bond 0.00430 ( 2) SS BOND : angle 0.72060 ( 4) hydrogen bonds : bond 0.03230 ( 391) hydrogen bonds : angle 4.33788 ( 1098) Misc. bond : bond 0.00016 ( 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 124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.294 Fit side-chains outliers start: 33 outliers final: 30 residues processed: 111 average time/residue: 0.0710 time to fit residues: 10.8966 Evaluate side-chains 121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 172 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 273 ASP 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 191 SER 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 84 THR Chi-restraints excluded: chain H residue 97 VAL 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: 0.9980 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 0.0070 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138217 restraints weight = 9965.789| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.43 r_work: 0.3422 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8066 Z= 0.103 Angle : 0.518 7.245 11012 Z= 0.263 Chirality : 0.041 0.197 1307 Planarity : 0.004 0.041 1397 Dihedral : 6.949 179.691 1168 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.48 % Allowed : 19.95 % 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 aren not related in a simple way. whole: 0.69 (0.27), residues: 1067 helix: 2.20 (0.28), residues: 362 sheet: 0.13 (0.32), residues: 296 loop : -0.87 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 18 TYR 0.016 0.001 TYR B 297 PHE 0.032 0.001 PHE H 68 TRP 0.008 0.001 TRP C 63 HIS 0.002 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8063) covalent geometry : angle 0.51833 (11008) SS BOND : bond 0.00368 ( 2) SS BOND : angle 0.61166 ( 4) hydrogen bonds : bond 0.02957 ( 391) hydrogen bonds : angle 4.22487 ( 1098) Misc. bond : bond 0.00012 ( 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: 26 poor density : 97 time to evaluate : 0.294 Fit side-chains REVERT: A 238 SER cc_start: 0.8041 (t) cc_final: 0.7632 (p) REVERT: A 265 MET cc_start: 0.8241 (tpp) cc_final: 0.7989 (tpp) outliers start: 26 outliers final: 24 residues processed: 113 average time/residue: 0.0980 time to fit residues: 15.0366 Evaluate side-chains 119 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 273 ASP 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 64 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP 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: 0.7980 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: 2.9990 chunk 66 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137273 restraints weight = 9918.659| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.42 r_work: 0.3414 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2253 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= 0.116 Angle : 0.537 8.406 11012 Z= 0.272 Chirality : 0.042 0.192 1307 Planarity : 0.004 0.041 1397 Dihedral : 6.964 179.429 1168 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.35 % Allowed : 20.62 % Favored : 76.04 % 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 aren not related in a simple way. whole: 0.67 (0.27), residues: 1067 helix: 2.18 (0.28), residues: 361 sheet: 0.13 (0.32), residues: 300 loop : -0.88 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 18 TYR 0.016 0.001 TYR B 297 PHE 0.035 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 covalent geometry : bond 0.00267 ( 8063) covalent geometry : angle 0.53660 (11008) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.69882 ( 4) hydrogen bonds : bond 0.03077 ( 391) hydrogen bonds : angle 4.24914 ( 1098) Misc. bond : bond 0.00013 ( 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 118 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.235 Fit side-chains REVERT: A 265 MET cc_start: 0.8240 (tpp) cc_final: 0.7978 (tpp) outliers start: 25 outliers final: 24 residues processed: 108 average time/residue: 0.0915 time to fit residues: 13.4276 Evaluate side-chains 117 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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 273 ASP 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 64 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP 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: 0.8980 chunk 77 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.160069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136022 restraints weight = 9926.905| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.37 r_work: 0.3435 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2305 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= 0.130 Angle : 0.549 7.984 11012 Z= 0.278 Chirality : 0.042 0.189 1307 Planarity : 0.004 0.041 1397 Dihedral : 7.011 179.363 1168 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.75 % Allowed : 20.35 % Favored : 75.90 % 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 aren not related in a simple way. whole: 0.62 (0.27), residues: 1067 helix: 2.15 (0.28), residues: 361 sheet: 0.11 (0.32), residues: 293 loop : -0.90 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 18 TYR 0.015 0.001 TYR B 297 PHE 0.036 0.001 PHE H 68 TRP 0.007 0.001 TRP C 63 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8063) covalent geometry : angle 0.54861 (11008) SS BOND : bond 0.00439 ( 2) SS BOND : angle 0.76910 ( 4) hydrogen bonds : bond 0.03203 ( 391) hydrogen bonds : angle 4.29587 ( 1098) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.58 seconds wall clock time: 37 minutes 12.46 seconds (2232.46 seconds total)