Starting phenix.real_space_refine on Wed Sep 17 07:30:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u3p_63823/09_2025/9u3p_63823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u3p_63823/09_2025/9u3p_63823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u3p_63823/09_2025/9u3p_63823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u3p_63823/09_2025/9u3p_63823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u3p_63823/09_2025/9u3p_63823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u3p_63823/09_2025/9u3p_63823.map" } resolution = 2.65 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= 0.002 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 4198 2.51 5 N 1148 2.21 5 O 1258 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6655 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3890 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 481} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.88, per 1000 atoms: 0.28 Number of scatterers: 6655 At special positions: 0 Unit cell: (90.06, 106.65, 119.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 3 15.00 Mg 1 11.99 O 1258 8.00 N 1148 7.00 C 4198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 323.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1554 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 52.8% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 313 through 336 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 411 through 433 Processing helix chain 'A' and resid 457 through 481 Processing helix chain 'A' and resid 511 through 523 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 549 through 555 Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 1013 through 1034 Processing helix chain 'A' and resid 1037 through 1045 Processing helix chain 'A' and resid 1066 through 1071 Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1078 through 1097 removed outlier: 3.629A pdb=" N LEU A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER A1097 " --> pdb=" O ASP A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1102 removed outlier: 3.540A pdb=" N SER A1102 " --> pdb=" O PRO A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1155 removed outlier: 3.551A pdb=" N ASN A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1201 Processing helix chain 'A' and resid 1209 through 1217 Processing helix chain 'A' and resid 1218 through 1220 No H-bonds generated for 'chain 'A' and resid 1218 through 1220' Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 87 through 113 removed outlier: 4.118A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.549A pdb=" N ARG B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 227 through 232 removed outlier: 4.015A pdb=" N ARG B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 251 through 255 removed outlier: 4.286A pdb=" N ASN B 254 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.994A pdb=" N ARG B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.591A pdb=" N PHE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 390 removed outlier: 4.338A pdb=" N ASP B 381 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 441 removed outlier: 7.283A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N MET A 387 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE A 499 " --> pdb=" O MET A 387 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 441 removed outlier: 7.283A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N MET A 387 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE A 499 " --> pdb=" O MET A 387 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N HIS A 530 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 488 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N SER A 532 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL A 490 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1104 through 1110 removed outlier: 5.187A pdb=" N LYS A1106 " --> pdb=" O ALA A1117 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA A1117 " --> pdb=" O LYS A1106 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A1108 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER A1056 " --> pdb=" O GLY A1170 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY A1170 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A1058 " --> pdb=" O ASN A1168 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN A1168 " --> pdb=" O GLY A1058 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A1060 " --> pdb=" O GLY A1166 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY A1166 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA A1062 " --> pdb=" O ARG A1164 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG A1164 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1104 through 1110 removed outlier: 5.187A pdb=" N LYS A1106 " --> pdb=" O ALA A1117 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA A1117 " --> pdb=" O LYS A1106 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A1108 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER A1056 " --> pdb=" O GLY A1170 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY A1170 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A1058 " --> pdb=" O ASN A1168 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN A1168 " --> pdb=" O GLY A1058 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A1060 " --> pdb=" O GLY A1166 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY A1166 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA A1062 " --> pdb=" O ARG A1164 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG A1164 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLN A1207 " --> pdb=" O LEU A1163 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A1165 " --> pdb=" O GLN A1207 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY A1235 " --> pdb=" O ASN A1230 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN A1230 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N MET A1237 " --> pdb=" O THR A1228 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR A1228 " --> pdb=" O MET A1237 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR A1239 " --> pdb=" O ARG A1226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 214 removed outlier: 6.355A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1068 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: 1.27 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2214 1.34 - 1.46: 1352 1.46 - 1.58: 3139 1.58 - 1.69: 5 1.69 - 1.81: 74 Bond restraints: 6784 Sorted by residual: bond pdb=" CB GLU A1210 " pdb=" CG GLU A1210 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.91e-01 bond pdb=" CB GLU B 157 " pdb=" CG GLU B 157 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.59e-01 bond pdb=" CB GLU A1211 " pdb=" CG GLU A1211 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.55e-01 bond pdb=" CG LEU A 429 " pdb=" CD2 LEU A 429 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.10e-01 bond pdb=" CB LEU A 429 " pdb=" CG LEU A 429 " ideal model delta sigma weight residual 1.530 1.515 0.015 2.00e-02 2.50e+03 5.92e-01 ... (remaining 6779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 9032 1.43 - 2.86: 95 2.86 - 4.29: 30 4.29 - 5.72: 2 5.72 - 7.15: 4 Bond angle restraints: 9163 Sorted by residual: angle pdb=" CA GLU A1210 " pdb=" CB GLU A1210 " pdb=" CG GLU A1210 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" C1' GSP B 501 " pdb=" C2' GSP B 501 " pdb=" C3' GSP B 501 " ideal model delta sigma weight residual 111.00 104.03 6.97 3.00e+00 1.11e-01 5.40e+00 angle pdb=" CB GLU B 157 " pdb=" CG GLU B 157 " pdb=" CD GLU B 157 " ideal model delta sigma weight residual 112.60 116.28 -3.68 1.70e+00 3.46e-01 4.68e+00 angle pdb=" CB GLU A1210 " pdb=" CG GLU A1210 " pdb=" CD GLU A1210 " ideal model delta sigma weight residual 112.60 116.27 -3.67 1.70e+00 3.46e-01 4.67e+00 angle pdb=" C ASP B 215 " pdb=" N LYS B 216 " pdb=" CA LYS B 216 " ideal model delta sigma weight residual 122.08 125.24 -3.16 1.47e+00 4.63e-01 4.63e+00 ... (remaining 9158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3478 17.89 - 35.78: 428 35.78 - 53.67: 143 53.67 - 71.57: 29 71.57 - 89.46: 10 Dihedral angle restraints: 4088 sinusoidal: 1679 harmonic: 2409 Sorted by residual: dihedral pdb=" O2G GSP B 501 " pdb=" O3B GSP B 501 " pdb=" PG GSP B 501 " pdb=" PB GSP B 501 " ideal model delta sinusoidal sigma weight residual 70.94 -12.61 83.56 1 2.00e+01 2.50e-03 2.13e+01 dihedral pdb=" CA ASP A1100 " pdb=" CB ASP A1100 " pdb=" CG ASP A1100 " pdb=" OD1 ASP A1100 " ideal model delta sinusoidal sigma weight residual -30.00 -89.26 59.26 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A 541 " pdb=" CB ASP A 541 " pdb=" CG ASP A 541 " pdb=" OD1 ASP A 541 " ideal model delta sinusoidal sigma weight residual -30.00 -87.37 57.37 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 673 0.034 - 0.068: 241 0.068 - 0.101: 52 0.101 - 0.135: 35 0.135 - 0.169: 2 Chirality restraints: 1003 Sorted by residual: chirality pdb=" C3' GSP B 501 " pdb=" C2' GSP B 501 " pdb=" C4' GSP B 501 " pdb=" O3' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CG LEU A 429 " pdb=" CB LEU A 429 " pdb=" CD1 LEU A 429 " pdb=" CD2 LEU A 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA LYS B 216 " pdb=" N LYS B 216 " pdb=" C LYS B 216 " pdb=" CB LYS B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1000 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1251 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A1252 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1252 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1252 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 483 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C MET A 483 " 0.020 2.00e-02 2.50e+03 pdb=" O MET A 483 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL A 484 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1109 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.05e+00 pdb=" C THR A1109 " 0.018 2.00e-02 2.50e+03 pdb=" O THR A1109 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE A1110 " -0.006 2.00e-02 2.50e+03 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 782 2.75 - 3.29: 6617 3.29 - 3.83: 12128 3.83 - 4.36: 14713 4.36 - 4.90: 23721 Nonbonded interactions: 57961 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 2.215 2.170 nonbonded pdb=" OG SER B 54 " pdb="MG MG B 502 " model vdw 2.219 2.170 nonbonded pdb=" NH1 ARG A 383 " pdb=" OE2 GLU A1094 " model vdw 2.220 3.120 nonbonded pdb=" OH TYR B 318 " pdb=" OD2 ASP B 343 " model vdw 2.221 3.040 nonbonded pdb=" O ALA B 48 " pdb=" OG SER B 51 " model vdw 2.282 3.040 ... (remaining 57956 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: 2.170 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.270 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:9.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.002 0.028 6784 Z= 0.102 Angle : 0.449 7.154 9163 Z= 0.240 Chirality : 0.040 0.169 1003 Planarity : 0.003 0.044 1185 Dihedral : 17.924 89.457 2534 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.77 % Allowed : 23.44 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.29), residues: 818 helix: 1.37 (0.26), residues: 373 sheet: 0.20 (0.48), residues: 109 loop : -0.12 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1033 TYR 0.010 0.001 TYR A 446 PHE 0.010 0.001 PHE A1061 TRP 0.012 0.002 TRP A 510 HIS 0.004 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 6784) covalent geometry : angle 0.44930 ( 9163) hydrogen bonds : bond 0.14366 ( 348) hydrogen bonds : angle 6.63143 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.287 Fit side-chains REVERT: A 475 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: A 1034 ASN cc_start: 0.8740 (t0) cc_final: 0.8492 (t0) outliers start: 20 outliers final: 16 residues processed: 109 average time/residue: 0.6687 time to fit residues: 76.1118 Evaluate side-chains 103 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 380 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN B 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128784 restraints weight = 7758.880| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.05 r_work: 0.3339 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6784 Z= 0.128 Angle : 0.469 7.916 9163 Z= 0.247 Chirality : 0.041 0.189 1003 Planarity : 0.003 0.041 1185 Dihedral : 7.372 88.167 945 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.22 % Allowed : 22.88 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.29), residues: 818 helix: 1.73 (0.26), residues: 380 sheet: -0.03 (0.49), residues: 100 loop : 0.17 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 374 TYR 0.013 0.001 TYR A 446 PHE 0.014 0.001 PHE A1067 TRP 0.009 0.001 TRP B 281 HIS 0.006 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6784) covalent geometry : angle 0.46909 ( 9163) hydrogen bonds : bond 0.04089 ( 348) hydrogen bonds : angle 4.94743 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.314 Fit side-chains REVERT: A 1115 MET cc_start: 0.8985 (ttt) cc_final: 0.8782 (ttt) REVERT: B 166 SER cc_start: 0.7682 (p) cc_final: 0.7449 (m) REVERT: B 317 ARG cc_start: 0.7436 (mtm110) cc_final: 0.7184 (mtp180) REVERT: B 389 ARG cc_start: 0.7087 (tmm160) cc_final: 0.6761 (tmm-80) outliers start: 16 outliers final: 9 residues processed: 106 average time/residue: 0.6456 time to fit residues: 71.5893 Evaluate side-chains 98 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN B 112 ASN B 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128074 restraints weight = 7640.685| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.05 r_work: 0.3318 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6784 Z= 0.131 Angle : 0.459 7.941 9163 Z= 0.241 Chirality : 0.041 0.191 1003 Planarity : 0.003 0.039 1185 Dihedral : 6.337 90.642 927 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.83 % Favored : 98.04 % Rotamer: Outliers : 2.50 % Allowed : 22.47 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.30), residues: 818 helix: 1.85 (0.26), residues: 380 sheet: -0.03 (0.49), residues: 101 loop : 0.12 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1033 TYR 0.013 0.001 TYR A 446 PHE 0.011 0.001 PHE A1067 TRP 0.008 0.001 TRP B 281 HIS 0.007 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6784) covalent geometry : angle 0.45944 ( 9163) hydrogen bonds : bond 0.03941 ( 348) hydrogen bonds : angle 4.70477 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.297 Fit side-chains REVERT: A 329 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7764 (tt) REVERT: A 1210 GLU cc_start: 0.8335 (tp30) cc_final: 0.7712 (tt0) REVERT: B 166 SER cc_start: 0.7572 (p) cc_final: 0.7343 (m) REVERT: B 317 ARG cc_start: 0.7459 (mtm110) cc_final: 0.7170 (mtp180) outliers start: 18 outliers final: 10 residues processed: 102 average time/residue: 0.6589 time to fit residues: 70.0525 Evaluate side-chains 99 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 181 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 47 optimal weight: 0.0370 chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 0.0370 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A1034 ASN B 112 ASN B 384 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.165266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.130207 restraints weight = 7700.287| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.97 r_work: 0.3351 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6784 Z= 0.108 Angle : 0.446 7.721 9163 Z= 0.234 Chirality : 0.041 0.185 1003 Planarity : 0.003 0.038 1185 Dihedral : 6.077 86.479 926 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.08 % Favored : 97.80 % Rotamer: Outliers : 2.22 % Allowed : 23.16 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.30), residues: 818 helix: 2.00 (0.26), residues: 380 sheet: 0.01 (0.49), residues: 101 loop : 0.13 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1033 TYR 0.013 0.001 TYR A 446 PHE 0.011 0.001 PHE A1061 TRP 0.007 0.001 TRP B 281 HIS 0.007 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 6784) covalent geometry : angle 0.44576 ( 9163) hydrogen bonds : bond 0.03676 ( 348) hydrogen bonds : angle 4.53106 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.247 Fit side-chains REVERT: A 329 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7746 (tt) REVERT: A 1038 TYR cc_start: 0.7676 (t80) cc_final: 0.7449 (t80) REVERT: B 166 SER cc_start: 0.7514 (p) cc_final: 0.7303 (m) REVERT: B 317 ARG cc_start: 0.7442 (mtm110) cc_final: 0.7151 (mtp180) REVERT: B 356 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6744 (mtm-85) outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 0.6574 time to fit residues: 70.0569 Evaluate side-chains 97 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN B 112 ASN B 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.163418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126779 restraints weight = 7840.804| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.79 r_work: 0.3315 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6784 Z= 0.147 Angle : 0.477 8.023 9163 Z= 0.249 Chirality : 0.042 0.193 1003 Planarity : 0.003 0.037 1185 Dihedral : 6.248 92.731 926 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.77 % Allowed : 22.88 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.30), residues: 818 helix: 1.92 (0.26), residues: 380 sheet: -0.01 (0.50), residues: 100 loop : 0.14 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1033 TYR 0.015 0.001 TYR A1114 PHE 0.012 0.001 PHE A1067 TRP 0.008 0.001 TRP B 281 HIS 0.007 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6784) covalent geometry : angle 0.47735 ( 9163) hydrogen bonds : bond 0.03931 ( 348) hydrogen bonds : angle 4.60539 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.258 Fit side-chains REVERT: A 329 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7763 (tt) REVERT: A 475 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: A 1210 GLU cc_start: 0.8303 (tp30) cc_final: 0.7704 (tt0) REVERT: B 166 SER cc_start: 0.7555 (p) cc_final: 0.7332 (m) REVERT: B 317 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7160 (mtp180) REVERT: B 356 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6760 (mtm-85) outliers start: 20 outliers final: 11 residues processed: 105 average time/residue: 0.6731 time to fit residues: 73.7353 Evaluate side-chains 102 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN B 112 ASN B 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.162550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125835 restraints weight = 7755.184| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.78 r_work: 0.3303 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6784 Z= 0.164 Angle : 0.497 8.106 9163 Z= 0.258 Chirality : 0.042 0.197 1003 Planarity : 0.003 0.036 1185 Dihedral : 6.382 98.663 926 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.33 % Allowed : 22.61 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.30), residues: 818 helix: 1.86 (0.26), residues: 379 sheet: -0.04 (0.48), residues: 110 loop : 0.12 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1033 TYR 0.016 0.002 TYR A1114 PHE 0.012 0.001 PHE A1067 TRP 0.008 0.001 TRP B 281 HIS 0.007 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6784) covalent geometry : angle 0.49670 ( 9163) hydrogen bonds : bond 0.04058 ( 348) hydrogen bonds : angle 4.66108 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.254 Fit side-chains REVERT: A 329 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7735 (tt) REVERT: A 475 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: B 166 SER cc_start: 0.7578 (p) cc_final: 0.7346 (m) REVERT: B 299 GLU cc_start: 0.7361 (tp30) cc_final: 0.7055 (tt0) REVERT: B 317 ARG cc_start: 0.7491 (mtm110) cc_final: 0.7181 (mtp180) REVERT: B 356 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6737 (mtm-85) outliers start: 24 outliers final: 13 residues processed: 109 average time/residue: 0.6648 time to fit residues: 75.7475 Evaluate side-chains 101 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN B 112 ASN B 261 ASN B 384 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.164733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128463 restraints weight = 7759.450| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.78 r_work: 0.3347 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6784 Z= 0.117 Angle : 0.464 7.794 9163 Z= 0.243 Chirality : 0.041 0.187 1003 Planarity : 0.003 0.036 1185 Dihedral : 5.995 90.819 926 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.22 % Allowed : 23.44 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.30), residues: 818 helix: 2.02 (0.26), residues: 379 sheet: -0.01 (0.48), residues: 111 loop : 0.10 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1033 TYR 0.013 0.001 TYR A 446 PHE 0.011 0.001 PHE A1061 TRP 0.008 0.001 TRP B 281 HIS 0.007 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6784) covalent geometry : angle 0.46439 ( 9163) hydrogen bonds : bond 0.03695 ( 348) hydrogen bonds : angle 4.44882 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.269 Fit side-chains REVERT: A 475 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7389 (mt0) REVERT: A 1210 GLU cc_start: 0.8229 (tp30) cc_final: 0.7659 (tt0) REVERT: B 166 SER cc_start: 0.7510 (p) cc_final: 0.7305 (m) REVERT: B 299 GLU cc_start: 0.7353 (tp30) cc_final: 0.7090 (tt0) REVERT: B 317 ARG cc_start: 0.7458 (mtm110) cc_final: 0.7165 (mtp180) REVERT: B 356 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6730 (mtm-85) outliers start: 16 outliers final: 8 residues processed: 101 average time/residue: 0.6844 time to fit residues: 72.2065 Evaluate side-chains 94 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 54 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN B 112 ASN B 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.164294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128558 restraints weight = 7717.473| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.03 r_work: 0.3325 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6784 Z= 0.133 Angle : 0.479 8.001 9163 Z= 0.250 Chirality : 0.042 0.189 1003 Planarity : 0.003 0.041 1185 Dihedral : 5.710 92.373 923 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.08 % Allowed : 23.58 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.30), residues: 818 helix: 1.95 (0.26), residues: 379 sheet: 0.03 (0.48), residues: 111 loop : 0.11 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 383 TYR 0.014 0.001 TYR A1114 PHE 0.011 0.001 PHE A1067 TRP 0.008 0.001 TRP A1030 HIS 0.007 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6784) covalent geometry : angle 0.47858 ( 9163) hydrogen bonds : bond 0.03798 ( 348) hydrogen bonds : angle 4.48449 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.264 Fit side-chains REVERT: A 475 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7412 (mt0) REVERT: A 1210 GLU cc_start: 0.8207 (tp30) cc_final: 0.7636 (tt0) REVERT: B 166 SER cc_start: 0.7539 (p) cc_final: 0.7323 (m) REVERT: B 299 GLU cc_start: 0.7389 (tp30) cc_final: 0.7120 (tt0) REVERT: B 317 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7177 (mtp180) REVERT: B 356 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6741 (mtm-85) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.7473 time to fit residues: 77.8221 Evaluate side-chains 95 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.0070 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN B 112 ASN B 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129949 restraints weight = 7750.734| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.78 r_work: 0.3350 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6784 Z= 0.115 Angle : 0.471 7.685 9163 Z= 0.246 Chirality : 0.041 0.183 1003 Planarity : 0.003 0.038 1185 Dihedral : 5.561 87.605 923 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.66 % Allowed : 24.13 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.30), residues: 818 helix: 1.98 (0.26), residues: 379 sheet: 0.05 (0.48), residues: 111 loop : 0.11 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 383 TYR 0.013 0.001 TYR A 446 PHE 0.010 0.001 PHE A1061 TRP 0.008 0.001 TRP A1158 HIS 0.007 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6784) covalent geometry : angle 0.47094 ( 9163) hydrogen bonds : bond 0.03630 ( 348) hydrogen bonds : angle 4.38455 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.235 Fit side-chains REVERT: A 391 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7854 (mm-30) REVERT: A 475 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: B 157 GLU cc_start: 0.7217 (mm-30) cc_final: 0.7003 (tp30) REVERT: B 166 SER cc_start: 0.7498 (p) cc_final: 0.7297 (m) REVERT: B 299 GLU cc_start: 0.7334 (tp30) cc_final: 0.7079 (tt0) REVERT: B 317 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7148 (mtp180) REVERT: B 356 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6750 (mtm-85) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 0.6766 time to fit residues: 69.1936 Evaluate side-chains 97 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 0.0070 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN B 112 ASN B 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.165822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130463 restraints weight = 7766.638| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.02 r_work: 0.3333 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6784 Z= 0.121 Angle : 0.475 7.709 9163 Z= 0.250 Chirality : 0.041 0.184 1003 Planarity : 0.003 0.036 1185 Dihedral : 5.568 86.984 923 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.53 % Allowed : 24.41 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.30), residues: 818 helix: 1.99 (0.26), residues: 379 sheet: 0.08 (0.48), residues: 111 loop : 0.13 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 383 TYR 0.013 0.001 TYR A1114 PHE 0.012 0.001 PHE A1061 TRP 0.008 0.001 TRP A1158 HIS 0.007 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6784) covalent geometry : angle 0.47506 ( 9163) hydrogen bonds : bond 0.03667 ( 348) hydrogen bonds : angle 4.39053 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.262 Fit side-chains REVERT: A 391 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7566 (mm-30) REVERT: A 475 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7381 (mt0) REVERT: B 157 GLU cc_start: 0.7222 (mm-30) cc_final: 0.7008 (tp30) REVERT: B 166 SER cc_start: 0.7485 (p) cc_final: 0.7277 (m) REVERT: B 299 GLU cc_start: 0.7366 (tp30) cc_final: 0.7104 (tt0) REVERT: B 317 ARG cc_start: 0.7487 (mtm110) cc_final: 0.7169 (mtp180) REVERT: B 356 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6769 (mtm-85) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.7288 time to fit residues: 71.3963 Evaluate side-chains 96 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN B 93 GLN B 112 ASN B 384 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131596 restraints weight = 7700.251| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.67 r_work: 0.3360 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6784 Z= 0.122 Angle : 0.479 7.712 9163 Z= 0.252 Chirality : 0.041 0.184 1003 Planarity : 0.003 0.036 1185 Dihedral : 5.559 86.810 923 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.94 % Allowed : 24.13 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.30), residues: 818 helix: 2.01 (0.26), residues: 379 sheet: 0.09 (0.48), residues: 111 loop : 0.13 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1033 TYR 0.013 0.001 TYR A 446 PHE 0.011 0.001 PHE A1061 TRP 0.008 0.001 TRP A1158 HIS 0.007 0.001 HIS A1248 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6784) covalent geometry : angle 0.47876 ( 9163) hydrogen bonds : bond 0.03668 ( 348) hydrogen bonds : angle 4.39061 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.65 seconds wall clock time: 52 minutes 5.91 seconds (3125.91 seconds total)