Starting phenix.real_space_refine on Thu Sep 18 20:06:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbh_11155/09_2025/6zbh_11155.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbh_11155/09_2025/6zbh_11155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zbh_11155/09_2025/6zbh_11155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbh_11155/09_2025/6zbh_11155.map" model { file = "/net/cci-nas-00/data/ceres_data/6zbh_11155/09_2025/6zbh_11155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbh_11155/09_2025/6zbh_11155.cif" } resolution = 3.6 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= -0.001 sd= 0.036 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: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 6191 2.51 5 N 1576 2.21 5 O 1841 1.98 5 H 9896 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 19523 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9553 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 14, 'TRANS': 547} Chain breaks: 4 Chain: "B" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1900 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "C" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4669 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Chain: "D" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3401 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain breaks: 1 Time building chain proxies: 3.48, per 1000 atoms: 0.18 Number of scatterers: 19523 At special positions: 0 Unit cell: (107.3, 137.344, 139.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 O 1841 8.00 N 1576 7.00 C 6191 6.00 H 9896 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=2.08 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 845 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 546.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 86.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.596A pdb=" N HIS A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 4.207A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 4.279A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.917A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.619A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 249 through 281 removed outlier: 4.118A pdb=" N ASP A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 321 removed outlier: 3.954A pdb=" N SER A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.508A pdb=" N ILE A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.736A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 495 removed outlier: 3.982A pdb=" N ARG A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 523 removed outlier: 3.728A pdb=" N LEU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.504A pdb=" N PHE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 616 removed outlier: 3.610A pdb=" N ASN A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 666 removed outlier: 4.267A pdb=" N LEU A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 664 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 712 removed outlier: 3.646A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 699 - end of helix Processing helix chain 'B' and resid 795 through 822 Processing helix chain 'B' and resid 825 through 831 removed outlier: 3.761A pdb=" N VAL B 831 " --> pdb=" O LYS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 840 Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 857 through 891 removed outlier: 3.686A pdb=" N MET B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 871 " --> pdb=" O SER B 867 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE B 877 " --> pdb=" O GLN B 873 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 880 " --> pdb=" O PHE B 876 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 882 " --> pdb=" O GLU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.952A pdb=" N LEU B 900 " --> pdb=" O HIS B 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 968 Processing helix chain 'C' and resid 970 through 972 No H-bonds generated for 'chain 'C' and resid 970 through 972' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 980 through 982 No H-bonds generated for 'chain 'C' and resid 980 through 982' Processing helix chain 'C' and resid 995 through 1010 removed outlier: 3.763A pdb=" N LYS C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1025 removed outlier: 3.597A pdb=" N LYS C1019 " --> pdb=" O ASN C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1031 Processing helix chain 'C' and resid 1033 through 1101 removed outlier: 3.532A pdb=" N GLU C1043 " --> pdb=" O ALA C1039 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C1056 " --> pdb=" O GLN C1052 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C1057 " --> pdb=" O LEU C1053 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C1097 " --> pdb=" O GLU C1093 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C1100 " --> pdb=" O LEU C1096 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1108 No H-bonds generated for 'chain 'C' and resid 1106 through 1108' Processing helix chain 'C' and resid 1109 through 1146 removed outlier: 3.695A pdb=" N PHE C1113 " --> pdb=" O PHE C1109 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C1119 " --> pdb=" O LYS C1115 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C1122 " --> pdb=" O GLU C1118 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C1143 " --> pdb=" O LYS C1139 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR C1144 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1178 removed outlier: 4.040A pdb=" N TYR C1166 " --> pdb=" O THR C1162 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA C1167 " --> pdb=" O GLU C1163 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C1175 " --> pdb=" O LYS C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1213 removed outlier: 3.629A pdb=" N LEU C1182 " --> pdb=" O ILE C1178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C1184 " --> pdb=" O GLY C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1235 removed outlier: 3.521A pdb=" N TYR C1235 " --> pdb=" O ALA C1231 " (cutoff:3.500A) Processing helix chain 'C' and resid 1236 through 1239 removed outlier: 3.537A pdb=" N LEU C1239 " --> pdb=" O GLU C1236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1236 through 1239' Processing helix chain 'D' and resid 1342 through 1346 Processing helix chain 'D' and resid 1347 through 1392 removed outlier: 3.617A pdb=" N SER D1357 " --> pdb=" O GLY D1353 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG D1384 " --> pdb=" O ARG D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1393 through 1399 removed outlier: 3.643A pdb=" N MET D1396 " --> pdb=" O SER D1393 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1415 removed outlier: 3.603A pdb=" N LEU D1415 " --> pdb=" O PHE D1412 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 3.670A pdb=" N PHE D1440 " --> pdb=" O ASN D1436 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU D1468 " --> pdb=" O LYS D1464 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D1469 " --> pdb=" O VAL D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1555 removed outlier: 3.547A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP D1544 " --> pdb=" O THR D1540 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 2112 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9894 1.04 - 1.23: 264 1.23 - 1.43: 3665 1.43 - 1.62: 5816 1.62 - 1.82: 32 Bond restraints: 19671 Sorted by residual: bond pdb=" N ILE A 218 " pdb=" CA ILE A 218 " ideal model delta sigma weight residual 1.454 1.485 -0.030 7.70e-03 1.69e+04 1.56e+01 bond pdb=" N LYS A 674 " pdb=" CA LYS A 674 " ideal model delta sigma weight residual 1.458 1.485 -0.027 7.40e-03 1.83e+04 1.34e+01 bond pdb=" C ILE A 613 " pdb=" O ILE A 613 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.23e-02 6.61e+03 1.29e+01 bond pdb=" N VAL C1105 " pdb=" CA VAL C1105 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" N VAL B 819 " pdb=" CA VAL B 819 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.23e-02 6.61e+03 1.09e+01 ... (remaining 19666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 30436 1.59 - 3.18: 4940 3.18 - 4.77: 377 4.77 - 6.36: 75 6.36 - 7.95: 6 Bond angle restraints: 35834 Sorted by residual: angle pdb=" N LYS B 815 " pdb=" CA LYS B 815 " pdb=" C LYS B 815 " ideal model delta sigma weight residual 111.36 104.94 6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" N TYR A 215 " pdb=" CA TYR A 215 " pdb=" C TYR A 215 " ideal model delta sigma weight residual 111.28 105.05 6.23 1.09e+00 8.42e-01 3.27e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.00 105.72 7.28 1.30e+00 5.92e-01 3.14e+01 angle pdb=" CA SER C1026 " pdb=" C SER C1026 " pdb=" O SER C1026 " ideal model delta sigma weight residual 120.92 114.84 6.08 1.12e+00 7.97e-01 2.95e+01 angle pdb=" N ASN A 467 " pdb=" CA ASN A 467 " pdb=" C ASN A 467 " ideal model delta sigma weight residual 111.36 117.25 -5.89 1.09e+00 8.42e-01 2.92e+01 ... (remaining 35829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 8385 17.83 - 35.66: 542 35.66 - 53.48: 123 53.48 - 71.31: 30 71.31 - 89.14: 13 Dihedral angle restraints: 9093 sinusoidal: 5058 harmonic: 4035 Sorted by residual: dihedral pdb=" CB CYS B 813 " pdb=" SG CYS B 813 " pdb=" SG CYS B 845 " pdb=" CB CYS B 845 " ideal model delta sinusoidal sigma weight residual 93.00 152.93 -59.93 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CA ASP A 466 " pdb=" C ASP A 466 " pdb=" N ASN A 467 " pdb=" CA ASN A 467 " ideal model delta harmonic sigma weight residual -180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU A 367 " pdb=" CG GLU A 367 " pdb=" CD GLU A 367 " pdb=" OE1 GLU A 367 " ideal model delta sinusoidal sigma weight residual 0.00 89.00 -89.00 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 779 0.057 - 0.115: 514 0.115 - 0.172: 151 0.172 - 0.230: 29 0.230 - 0.287: 3 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA VAL C1105 " pdb=" N VAL C1105 " pdb=" C VAL C1105 " pdb=" CB VAL C1105 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE D1401 " pdb=" N ILE D1401 " pdb=" C ILE D1401 " pdb=" CB ILE D1401 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL A 39 " pdb=" N VAL A 39 " pdb=" C VAL A 39 " pdb=" CB VAL A 39 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1473 not shown) Planarity restraints: 2771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C1099 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LEU C1099 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU C1099 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN C1100 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 217 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.32e+00 pdb=" C GLN A 217 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN A 217 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 218 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 327 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C ASN A 327 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN A 327 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 328 " -0.015 2.00e-02 2.50e+03 ... (remaining 2768 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 2661 2.29 - 2.87: 46133 2.87 - 3.45: 48298 3.45 - 4.02: 62136 4.02 - 4.60: 98778 Nonbonded interactions: 258006 Sorted by model distance: nonbonded pdb=" O GLU A 582 " pdb="HD22 ASN A 586 " model vdw 1.717 2.450 nonbonded pdb=" HZ3 LYS C1064 " pdb=" O SER C1150 " model vdw 1.717 2.450 nonbonded pdb=" O THR D1505 " pdb="HD22 ASN D1509 " model vdw 1.722 2.450 nonbonded pdb=" O ASN A 260 " pdb=" HG1 THR A 263 " model vdw 1.732 2.450 nonbonded pdb=" O TYR A 150 " pdb=" HG1 THR A 153 " model vdw 1.736 2.450 ... (remaining 258001 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 group one per residue 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.010 0.054 9777 Z= 0.725 Angle : 1.215 35.748 13115 Z= 0.865 Chirality : 0.076 0.287 1476 Planarity : 0.006 0.043 1647 Dihedral : 13.653 89.139 3843 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.24), residues: 1139 helix: 0.84 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -0.25 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 546 TYR 0.026 0.003 TYR A 683 PHE 0.015 0.003 PHE C1238 HIS 0.005 0.001 HIS D1400 Details of bonding type rmsd covalent geometry : bond 0.01006 ( 9775) covalent geometry : angle 1.17283 (13111) SS BOND : bond 0.03461 ( 2) SS BOND : angle 18.17792 ( 4) hydrogen bonds : bond 0.17231 ( 719) hydrogen bonds : angle 5.82594 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.9249 (tt0) cc_final: 0.9000 (tp40) REVERT: A 662 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 972 ASP cc_start: 0.8440 (m-30) cc_final: 0.7282 (t0) REVERT: C 1013 TYR cc_start: 0.7799 (t80) cc_final: 0.7562 (t80) REVERT: D 1377 LEU cc_start: 0.9148 (mp) cc_final: 0.8904 (mt) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2805 time to fit residues: 80.3371 Evaluate side-chains 97 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 365 HIS A 709 GLN B 821 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.060271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.050996 restraints weight = 163974.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.052876 restraints weight = 63962.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.054016 restraints weight = 35266.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.054761 restraints weight = 23782.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.055187 restraints weight = 18219.953| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9777 Z= 0.145 Angle : 0.566 5.699 13115 Z= 0.316 Chirality : 0.034 0.137 1476 Planarity : 0.004 0.038 1647 Dihedral : 4.180 24.614 1231 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.00 % Allowed : 6.97 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.84 (0.24), residues: 1139 helix: 1.61 (0.17), residues: 904 sheet: None (None), residues: 0 loop : -0.12 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1384 TYR 0.020 0.001 TYR D1455 PHE 0.011 0.001 PHE C1014 HIS 0.006 0.001 HIS B 896 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9775) covalent geometry : angle 0.56439 (13111) SS BOND : bond 0.01268 ( 2) SS BOND : angle 2.42609 ( 4) hydrogen bonds : bond 0.05721 ( 719) hydrogen bonds : angle 4.11006 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8789 (t0) cc_final: 0.8380 (m-30) REVERT: A 662 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7705 (tm-30) REVERT: B 846 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.6932 (t0) REVERT: C 1053 LEU cc_start: 0.9023 (tt) cc_final: 0.8525 (mt) REVERT: C 1078 ASP cc_start: 0.8670 (m-30) cc_final: 0.8345 (m-30) outliers start: 11 outliers final: 7 residues processed: 112 average time/residue: 0.2495 time to fit residues: 37.6479 Evaluate side-chains 85 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 640 GLN B 821 ASN B 856 ASN C1104 ASN C1183 ASN D1400 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.056433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046659 restraints weight = 180202.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.048496 restraints weight = 74432.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.049628 restraints weight = 43092.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.050341 restraints weight = 30291.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.050793 restraints weight = 23983.954| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9777 Z= 0.241 Angle : 0.591 5.515 13115 Z= 0.337 Chirality : 0.035 0.197 1476 Planarity : 0.003 0.033 1647 Dihedral : 4.129 30.259 1231 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.45 % Allowed : 7.79 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.91 (0.24), residues: 1139 helix: 1.70 (0.16), residues: 916 sheet: None (None), residues: 0 loop : -0.44 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 577 TYR 0.018 0.002 TYR D1455 PHE 0.011 0.001 PHE C1021 HIS 0.004 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 9775) covalent geometry : angle 0.58876 (13111) SS BOND : bond 0.01931 ( 2) SS BOND : angle 2.78173 ( 4) hydrogen bonds : bond 0.05105 ( 719) hydrogen bonds : angle 4.23535 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 846 ASP cc_start: 0.7957 (t0) cc_final: 0.7284 (t0) outliers start: 16 outliers final: 11 residues processed: 91 average time/residue: 0.2290 time to fit residues: 28.7070 Evaluate side-chains 75 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1011 ASP Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Chi-restraints excluded: chain D residue 1471 GLU Chi-restraints excluded: chain D residue 1507 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 821 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.057360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.047761 restraints weight = 174446.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.049585 restraints weight = 71515.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.050721 restraints weight = 41310.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.051383 restraints weight = 28882.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.051873 restraints weight = 23092.263| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9777 Z= 0.119 Angle : 0.493 8.078 13115 Z= 0.270 Chirality : 0.032 0.153 1476 Planarity : 0.003 0.033 1647 Dihedral : 3.867 27.054 1231 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.45 % Allowed : 8.24 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.66 (0.24), residues: 1139 helix: 2.21 (0.17), residues: 914 sheet: None (None), residues: 0 loop : -0.07 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1384 TYR 0.011 0.001 TYR B 816 PHE 0.010 0.001 PHE C1014 HIS 0.003 0.001 HIS B 896 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9775) covalent geometry : angle 0.48746 (13111) SS BOND : bond 0.00168 ( 2) SS BOND : angle 4.15334 ( 4) hydrogen bonds : bond 0.04655 ( 719) hydrogen bonds : angle 3.80903 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8802 (t0) cc_final: 0.8458 (m-30) REVERT: A 662 GLN cc_start: 0.8318 (tm-30) cc_final: 0.8052 (tm-30) REVERT: B 846 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7292 (t70) REVERT: D 1496 PHE cc_start: 0.7353 (m-80) cc_final: 0.6900 (m-80) outliers start: 16 outliers final: 12 residues processed: 84 average time/residue: 0.2162 time to fit residues: 25.5242 Evaluate side-chains 74 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 1397 GLN Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Chi-restraints excluded: chain D residue 1471 GLU Chi-restraints excluded: chain D residue 1507 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 821 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.056548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.046889 restraints weight = 188877.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.048704 restraints weight = 82553.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.049848 restraints weight = 49078.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.050577 restraints weight = 34816.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.051041 restraints weight = 27595.436| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9777 Z= 0.116 Angle : 0.482 8.769 13115 Z= 0.263 Chirality : 0.032 0.166 1476 Planarity : 0.003 0.033 1647 Dihedral : 3.752 34.324 1231 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.18 % Allowed : 8.88 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 3.01 (0.25), residues: 1139 helix: 2.46 (0.17), residues: 913 sheet: None (None), residues: 0 loop : 0.00 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1384 TYR 0.012 0.001 TYR D1455 PHE 0.010 0.001 PHE C1014 HIS 0.003 0.001 HIS B 896 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9775) covalent geometry : angle 0.47560 (13111) SS BOND : bond 0.00544 ( 2) SS BOND : angle 4.58316 ( 4) hydrogen bonds : bond 0.04404 ( 719) hydrogen bonds : angle 3.67110 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8704 (t0) cc_final: 0.8417 (m-30) REVERT: A 662 GLN cc_start: 0.8321 (tm-30) cc_final: 0.8043 (tm-30) REVERT: D 1496 PHE cc_start: 0.7458 (m-80) cc_final: 0.7053 (m-80) outliers start: 13 outliers final: 13 residues processed: 76 average time/residue: 0.2213 time to fit residues: 24.0872 Evaluate side-chains 75 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 1397 GLN Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Chi-restraints excluded: chain D residue 1507 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.055465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.045852 restraints weight = 190476.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.047619 restraints weight = 83857.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.048726 restraints weight = 50128.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.049427 restraints weight = 35777.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.049868 restraints weight = 28535.746| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9777 Z= 0.182 Angle : 0.505 7.472 13115 Z= 0.284 Chirality : 0.032 0.133 1476 Planarity : 0.003 0.031 1647 Dihedral : 3.639 23.759 1231 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.63 % Allowed : 9.24 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.98 (0.24), residues: 1139 helix: 2.47 (0.17), residues: 915 sheet: None (None), residues: 0 loop : -0.16 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 470 TYR 0.011 0.001 TYR C1013 PHE 0.009 0.001 PHE D1496 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9775) covalent geometry : angle 0.49990 (13111) SS BOND : bond 0.00381 ( 2) SS BOND : angle 4.25838 ( 4) hydrogen bonds : bond 0.04327 ( 719) hydrogen bonds : angle 3.82136 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8152 (tm-30) REVERT: D 1496 PHE cc_start: 0.7349 (m-80) cc_final: 0.7069 (m-80) outliers start: 18 outliers final: 15 residues processed: 78 average time/residue: 0.2163 time to fit residues: 23.9861 Evaluate side-chains 74 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1011 ASP Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 1397 GLN Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Chi-restraints excluded: chain D residue 1507 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.055906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.046259 restraints weight = 190391.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.048062 restraints weight = 83352.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.049190 restraints weight = 49527.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.049904 restraints weight = 35322.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.050361 restraints weight = 28095.727| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9777 Z= 0.115 Angle : 0.461 6.870 13115 Z= 0.253 Chirality : 0.031 0.135 1476 Planarity : 0.003 0.033 1647 Dihedral : 3.470 18.465 1231 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.45 % Allowed : 9.60 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.38 (0.25), residues: 1139 helix: 2.71 (0.17), residues: 917 sheet: None (None), residues: 0 loop : 0.14 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1384 TYR 0.018 0.001 TYR D1455 PHE 0.009 0.001 PHE C1014 HIS 0.003 0.001 HIS B 896 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9775) covalent geometry : angle 0.45963 (13111) SS BOND : bond 0.00855 ( 2) SS BOND : angle 1.81014 ( 4) hydrogen bonds : bond 0.04141 ( 719) hydrogen bonds : angle 3.57476 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8740 (t0) cc_final: 0.8380 (m-30) REVERT: A 662 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8130 (tm-30) outliers start: 16 outliers final: 14 residues processed: 72 average time/residue: 0.2215 time to fit residues: 22.9763 Evaluate side-chains 70 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1011 ASP Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 1397 GLN Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Chi-restraints excluded: chain D residue 1507 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1397 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 = 0.3600 r_free = 0.3600 target = 0.055163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.045629 restraints weight = 192074.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.047378 restraints weight = 84539.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.048484 restraints weight = 50558.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.049184 restraints weight = 35971.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.049635 restraints weight = 28579.793| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9777 Z= 0.158 Angle : 0.485 6.501 13115 Z= 0.271 Chirality : 0.031 0.132 1476 Planarity : 0.003 0.030 1647 Dihedral : 3.428 17.451 1231 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.36 % Allowed : 10.14 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.34 (0.25), residues: 1139 helix: 2.72 (0.17), residues: 915 sheet: None (None), residues: 0 loop : 0.00 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 470 TYR 0.017 0.001 TYR C1013 PHE 0.009 0.001 PHE C1014 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9775) covalent geometry : angle 0.48441 (13111) SS BOND : bond 0.00246 ( 2) SS BOND : angle 1.02840 ( 4) hydrogen bonds : bond 0.04086 ( 719) hydrogen bonds : angle 3.65611 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8768 (t0) cc_final: 0.8367 (m-30) REVERT: A 662 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 1080 MET cc_start: 0.9084 (tpp) cc_final: 0.8744 (tpp) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.1998 time to fit residues: 19.1083 Evaluate side-chains 65 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1011 ASP Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 1397 GLN Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Chi-restraints excluded: chain D residue 1507 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 81 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1397 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 = 0.3586 r_free = 0.3586 target = 0.054596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.045061 restraints weight = 193392.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.046790 restraints weight = 85417.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.047883 restraints weight = 50999.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048574 restraints weight = 36426.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.048979 restraints weight = 29076.920| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9777 Z= 0.204 Angle : 0.512 8.413 13115 Z= 0.291 Chirality : 0.032 0.142 1476 Planarity : 0.003 0.031 1647 Dihedral : 3.470 16.674 1231 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.27 % Allowed : 10.42 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.14 (0.24), residues: 1139 helix: 2.54 (0.16), residues: 927 sheet: None (None), residues: 0 loop : -0.03 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 470 TYR 0.018 0.001 TYR D1455 PHE 0.010 0.001 PHE C1021 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9775) covalent geometry : angle 0.51223 (13111) SS BOND : bond 0.00284 ( 2) SS BOND : angle 0.71211 ( 4) hydrogen bonds : bond 0.04133 ( 719) hydrogen bonds : angle 3.80984 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7955 (tm-30) REVERT: C 1080 MET cc_start: 0.9141 (tpp) cc_final: 0.8786 (tpp) outliers start: 14 outliers final: 14 residues processed: 63 average time/residue: 0.2016 time to fit residues: 18.6184 Evaluate side-chains 65 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1011 ASP Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Chi-restraints excluded: chain D residue 1507 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 2 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.055515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.045991 restraints weight = 189613.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.047764 restraints weight = 83150.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.048887 restraints weight = 49371.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.049585 restraints weight = 35148.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.050045 restraints weight = 27879.145| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9777 Z= 0.103 Angle : 0.462 7.851 13115 Z= 0.251 Chirality : 0.031 0.132 1476 Planarity : 0.003 0.032 1647 Dihedral : 3.376 16.671 1231 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.27 % Allowed : 10.87 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.64 (0.25), residues: 1139 helix: 2.89 (0.16), residues: 924 sheet: None (None), residues: 0 loop : 0.14 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1384 TYR 0.019 0.001 TYR D1455 PHE 0.011 0.001 PHE C1014 HIS 0.004 0.001 HIS B 896 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9775) covalent geometry : angle 0.46149 (13111) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.54445 ( 4) hydrogen bonds : bond 0.04002 ( 719) hydrogen bonds : angle 3.44600 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8764 (t0) cc_final: 0.8436 (m-30) REVERT: A 662 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 1080 MET cc_start: 0.9146 (tpp) cc_final: 0.8805 (tpp) outliers start: 14 outliers final: 13 residues processed: 70 average time/residue: 0.2047 time to fit residues: 20.9658 Evaluate side-chains 65 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 1397 GLN Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Chi-restraints excluded: chain D residue 1507 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.057622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.048499 restraints weight = 188814.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.050295 restraints weight = 79175.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.051422 restraints weight = 45301.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.052146 restraints weight = 31159.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.052615 restraints weight = 24083.226| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.331 9777 Z= 0.283 Angle : 0.822 59.199 13115 Z= 0.497 Chirality : 0.036 0.714 1476 Planarity : 0.003 0.032 1647 Dihedral : 3.380 16.659 1231 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.27 % Allowed : 11.14 % Favored : 87.59 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: 3.64 (0.25), residues: 1139 helix: 2.89 (0.16), residues: 924 sheet: None (None), residues: 0 loop : 0.15 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1384 TYR 0.017 0.001 TYR D1455 PHE 0.010 0.001 PHE C1014 HIS 0.004 0.001 HIS B 896 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 9775) covalent geometry : angle 0.82195 (13111) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.55489 ( 4) hydrogen bonds : bond 0.04007 ( 719) hydrogen bonds : angle 3.44706 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.14 seconds wall clock time: 50 minutes 33.33 seconds (3033.33 seconds total)