Starting phenix.real_space_refine on Fri Jun 6 20:07:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpt_34943/06_2025/8hpt_34943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpt_34943/06_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_34943/06_2025/8hpt_34943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpt_34943/06_2025/8hpt_34943.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpt_34943/06_2025/8hpt_34943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpt_34943/06_2025/8hpt_34943.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU: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: {'ZAL:plan-1': 1, 'ALC:plan-1': 1, 'MEA:plan-2': 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: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} 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: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 8, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 7} 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: {'GLU:plan': 2, 'ARG: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: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 5.77, per 1000 atoms: 0.73 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: 2.50 Conformation dependent library (CDL) restraints added in 1.0 seconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAR D 406 " Input volumes are d-peptide like pdb=" CB ZAL D 404 " 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: 1.02 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: 2.13 Time building geometry restraints manager: 2.63 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: 2.790 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.310 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- 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 : 6.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.031 0.001 TRP A 268 HIS 0.003 0.001 HIS B 189 PHE 0.025 0.001 PHE H 68 TYR 0.017 0.001 TYR B 297 ARG 0.006 0.001 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.15889 ( 391) hydrogen bonds : angle 6.27360 ( 1098) SS BOND : bond 0.00332 ( 2) SS BOND : angle 1.14157 ( 4) covalent geometry : bond 0.00275 ( 8063) covalent geometry : angle 0.59741 (11008) 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 : 0.831 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 96 average time/residue: 0.2096 time to fit residues: 27.2934 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 : 0.861 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.0270 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.175213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147312 restraints weight = 10306.799| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.82 r_work: 0.3555 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0934 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= 0.133 Angle : 0.564 7.675 11012 Z= 0.290 Chirality : 0.042 0.190 1307 Planarity : 0.005 0.058 1397 Dihedral : 7.246 173.474 1169 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.20 % Allowed : 13.12 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.27), residues: 1067 helix: 2.07 (0.29), residues: 366 sheet: 0.02 (0.32), residues: 297 loop : -1.09 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.005 0.001 HIS C 142 PHE 0.023 0.001 PHE H 68 TYR 0.015 0.001 TYR H 190 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 391) hydrogen bonds : angle 4.73474 ( 1098) SS BOND : bond 0.00486 ( 2) SS BOND : angle 1.21456 ( 4) covalent geometry : bond 0.00302 ( 8063) covalent geometry : angle 0.56373 (11008) Misc. bond : bond 0.00026 ( 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: 9 poor density : 98 time to evaluate : 0.975 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 105 average time/residue: 0.1904 time to fit residues: 28.0542 Evaluate side-chains 102 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.6980 chunk 14 optimal weight: 0.0370 chunk 104 optimal weight: 1.9990 chunk 7 optimal weight: 0.0020 chunk 2 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 overall best weight: 0.3066 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.177126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149112 restraints weight = 10466.177| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.83 r_work: 0.3573 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1201 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= 0.103 Angle : 0.520 7.871 11012 Z= 0.265 Chirality : 0.040 0.162 1307 Planarity : 0.004 0.055 1397 Dihedral : 7.181 178.184 1169 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.74 % Allowed : 15.26 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.27), residues: 1067 helix: 2.15 (0.28), residues: 364 sheet: 0.17 (0.32), residues: 294 loop : -1.02 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.002 0.001 HIS B 189 PHE 0.017 0.001 PHE H 68 TYR 0.014 0.001 TYR H 190 ARG 0.005 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 391) hydrogen bonds : angle 4.35861 ( 1098) SS BOND : bond 0.00410 ( 2) SS BOND : angle 0.84934 ( 4) covalent geometry : bond 0.00225 ( 8063) covalent geometry : angle 0.51978 (11008) Misc. bond : bond 0.00002 ( 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: 13 poor density : 107 time to evaluate : 0.795 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.2051 time to fit residues: 31.8298 Evaluate side-chains 113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 243 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.0070 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.176366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148706 restraints weight = 10376.776| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.77 r_work: 0.3578 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8066 Z= 0.106 Angle : 0.512 7.251 11012 Z= 0.262 Chirality : 0.041 0.155 1307 Planarity : 0.004 0.044 1397 Dihedral : 7.003 179.850 1168 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.68 % Allowed : 16.73 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1067 helix: 2.25 (0.28), residues: 363 sheet: 0.19 (0.32), residues: 298 loop : -1.02 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 169 HIS 0.003 0.001 HIS C 142 PHE 0.022 0.001 PHE H 68 TYR 0.015 0.001 TYR B 297 ARG 0.006 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 391) hydrogen bonds : angle 4.22442 ( 1098) SS BOND : bond 0.00399 ( 2) SS BOND : angle 0.74346 ( 4) covalent geometry : bond 0.00234 ( 8063) covalent geometry : angle 0.51231 (11008) Misc. bond : bond 0.00004 ( 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 121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.857 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.2190 time to fit residues: 33.3249 Evaluate side-chains 116 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 172 PHE 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 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 68 PHE Chi-restraints excluded: chain H residue 91 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.170418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141995 restraints weight = 10347.650| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.82 r_work: 0.3466 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8066 Z= 0.183 Angle : 0.589 7.386 11012 Z= 0.302 Chirality : 0.043 0.158 1307 Planarity : 0.004 0.044 1397 Dihedral : 7.201 178.679 1168 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.35 % Allowed : 18.07 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1067 helix: 2.06 (0.28), residues: 364 sheet: 0.08 (0.31), residues: 302 loop : -1.12 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 256 HIS 0.004 0.001 HIS C 142 PHE 0.037 0.002 PHE H 68 TYR 0.017 0.001 TYR H 190 ARG 0.006 0.001 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 391) hydrogen bonds : angle 4.49934 ( 1098) SS BOND : bond 0.00581 ( 2) SS BOND : angle 1.10123 ( 4) covalent geometry : bond 0.00440 ( 8063) covalent geometry : angle 0.58849 (11008) Misc. bond : bond 0.00005 ( 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 129 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.900 Fit side-chains outliers start: 25 outliers final: 21 residues processed: 119 average time/residue: 0.2001 time to fit residues: 32.9073 Evaluate side-chains 121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 191 SER 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 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 7 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141986 restraints weight = 10331.011| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.69 r_work: 0.3478 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8066 Z= 0.166 Angle : 0.570 7.259 11012 Z= 0.294 Chirality : 0.043 0.184 1307 Planarity : 0.004 0.042 1397 Dihedral : 7.170 178.731 1168 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.75 % Allowed : 18.74 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 1067 helix: 2.02 (0.28), residues: 360 sheet: 0.05 (0.32), residues: 295 loop : -1.09 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 63 HIS 0.004 0.001 HIS C 142 PHE 0.037 0.002 PHE H 68 TYR 0.015 0.001 TYR H 190 ARG 0.008 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 391) hydrogen bonds : angle 4.45858 ( 1098) SS BOND : bond 0.00540 ( 2) SS BOND : angle 0.98159 ( 4) covalent geometry : bond 0.00396 ( 8063) covalent geometry : angle 0.56993 (11008) Misc. bond : bond 0.00012 ( 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 131 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.644 Fit side-chains outliers start: 28 outliers final: 24 residues processed: 119 average time/residue: 0.2282 time to fit residues: 36.9389 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 : 1.108 ------------------------------------------------------------------------------- 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 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 275 SER Chi-restraints excluded: chain C residue 327 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 67 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.160395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135286 restraints weight = 10043.428| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.43 r_work: 0.3419 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2041 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 : 0.526 7.258 11012 Z= 0.269 Chirality : 0.041 0.208 1307 Planarity : 0.004 0.041 1397 Dihedral : 7.057 179.386 1168 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.35 % Allowed : 19.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 1067 helix: 2.12 (0.28), residues: 361 sheet: 0.04 (0.32), residues: 296 loop : -0.98 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.007 0.001 HIS C 183 PHE 0.033 0.001 PHE H 68 TYR 0.013 0.001 TYR H 190 ARG 0.008 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 391) hydrogen bonds : angle 4.30184 ( 1098) SS BOND : bond 0.00423 ( 2) SS BOND : angle 0.70655 ( 4) covalent geometry : bond 0.00263 ( 8063) covalent geometry : angle 0.52573 (11008) 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 131 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.051 Fit side-chains outliers start: 25 outliers final: 21 residues processed: 120 average time/residue: 0.2318 time to fit residues: 38.4506 Evaluate side-chains 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 5 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.159934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135757 restraints weight = 10009.101| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.46 r_work: 0.3405 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2120 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= 0.124 Angle : 0.542 7.242 11012 Z= 0.276 Chirality : 0.042 0.191 1307 Planarity : 0.004 0.041 1397 Dihedral : 7.033 179.301 1168 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.61 % Allowed : 20.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 1067 helix: 2.11 (0.28), residues: 361 sheet: 0.01 (0.32), residues: 300 loop : -0.95 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.005 0.001 HIS C 183 PHE 0.034 0.001 PHE H 68 TYR 0.014 0.001 TYR H 190 ARG 0.008 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 391) hydrogen bonds : angle 4.28027 ( 1098) SS BOND : bond 0.00444 ( 2) SS BOND : angle 0.76048 ( 4) covalent geometry : bond 0.00286 ( 8063) covalent geometry : angle 0.54196 (11008) Misc. bond : bond 0.00013 ( 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: 27 poor density : 97 time to evaluate : 0.794 Fit side-chains REVERT: A 265 MET cc_start: 0.8316 (tpp) cc_final: 0.8051 (tpp) outliers start: 27 outliers final: 25 residues processed: 112 average time/residue: 0.1987 time to fit residues: 31.0553 Evaluate side-chains 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 172 PHE Chi-restraints excluded: chain A residue 205 ILE 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 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 7 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.159585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134809 restraints weight = 10102.391| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.40 r_work: 0.3402 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2215 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 : 0.544 7.247 11012 Z= 0.279 Chirality : 0.042 0.173 1307 Planarity : 0.004 0.043 1397 Dihedral : 7.049 179.251 1168 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.88 % Allowed : 19.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1067 helix: 2.08 (0.28), residues: 361 sheet: -0.01 (0.32), residues: 302 loop : -0.92 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 63 HIS 0.003 0.001 HIS C 183 PHE 0.036 0.001 PHE H 68 TYR 0.014 0.001 TYR H 190 ARG 0.006 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 391) hydrogen bonds : angle 4.30933 ( 1098) SS BOND : bond 0.00454 ( 2) SS BOND : angle 0.78063 ( 4) covalent geometry : bond 0.00312 ( 8063) covalent geometry : angle 0.54407 (11008) Misc. bond : bond 0.00016 ( 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 128 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.046 Fit side-chains REVERT: A 265 MET cc_start: 0.8310 (tpp) cc_final: 0.8048 (tpp) outliers start: 29 outliers final: 26 residues processed: 115 average time/residue: 0.2056 time to fit residues: 32.5312 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 : 0.862 ------------------------------------------------------------------------------- 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 172 PHE Chi-restraints excluded: chain A residue 205 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 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 = 0.3811 r_free = 0.3811 target = 0.159544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134319 restraints weight = 9987.060| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.41 r_work: 0.3402 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2272 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= 0.130 Angle : 0.550 8.834 11012 Z= 0.279 Chirality : 0.042 0.170 1307 Planarity : 0.004 0.043 1397 Dihedral : 7.036 179.341 1168 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.75 % Allowed : 20.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 1067 helix: 2.09 (0.28), residues: 361 sheet: 0.03 (0.32), residues: 301 loop : -0.93 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 63 HIS 0.004 0.001 HIS C 183 PHE 0.037 0.001 PHE H 68 TYR 0.014 0.001 TYR H 190 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 391) hydrogen bonds : angle 4.31806 ( 1098) SS BOND : bond 0.00459 ( 2) SS BOND : angle 0.77221 ( 4) covalent geometry : bond 0.00304 ( 8063) covalent geometry : angle 0.54976 (11008) Misc. bond : bond 0.00015 ( 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 128 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.978 Fit side-chains REVERT: A 265 MET cc_start: 0.8299 (tpp) cc_final: 0.8042 (tpp) outliers start: 28 outliers final: 26 residues processed: 116 average time/residue: 0.1987 time to fit residues: 31.7540 Evaluate side-chains 125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 172 PHE Chi-restraints excluded: chain A residue 205 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.159016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133893 restraints weight = 9988.025| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.39 r_work: 0.3409 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2357 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= 0.142 Angle : 0.562 7.966 11012 Z= 0.285 Chirality : 0.042 0.166 1307 Planarity : 0.004 0.044 1397 Dihedral : 7.063 179.304 1168 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.88 % Allowed : 19.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 1067 helix: 2.10 (0.28), residues: 361 sheet: -0.01 (0.32), residues: 300 loop : -0.93 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 63 HIS 0.003 0.001 HIS C 142 PHE 0.039 0.001 PHE H 68 TYR 0.015 0.001 TYR H 190 ARG 0.010 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 391) hydrogen bonds : angle 4.34875 ( 1098) SS BOND : bond 0.00470 ( 2) SS BOND : angle 0.83075 ( 4) covalent geometry : bond 0.00335 ( 8063) covalent geometry : angle 0.56188 (11008) Misc. bond : bond 0.00017 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4597.20 seconds wall clock time: 80 minutes 59.28 seconds (4859.28 seconds total)