Starting phenix.real_space_refine on Mon Mar 18 00:19:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbh_11155/03_2024/6zbh_11155.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbh_11155/03_2024/6zbh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbh_11155/03_2024/6zbh_11155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbh_11155/03_2024/6zbh_11155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbh_11155/03_2024/6zbh_11155.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbh_11155/03_2024/6zbh_11155.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 8.13, per 1000 atoms: 0.42 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 - 3.50 Amino acid : False - 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: 15.26 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.24 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: 6.33 Time building geometry restraints manager: 15.80 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: 99.51 - 106.02: 314 106.02 - 112.53: 23310 112.53 - 119.04: 4840 119.04 - 125.55: 7181 125.55 - 132.06: 189 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 1.850 nonbonded pdb=" HZ3 LYS C1064 " pdb=" O SER C1150 " model vdw 1.717 1.850 nonbonded pdb=" O THR D1505 " pdb="HD22 ASN D1509 " model vdw 1.722 1.850 nonbonded pdb=" O ASN A 260 " pdb=" HG1 THR A 263 " model vdw 1.732 1.850 nonbonded pdb=" O TYR A 150 " pdb=" HG1 THR A 153 " model vdw 1.736 1.850 ... (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 ========== 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.280 Extract box with map and model: 6.010 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 58.240 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.230 ------------------------------------------------------------------------------- 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 9775 Z= 0.638 Angle : 1.173 7.448 13111 Z= 0.852 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (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 HIS 0.005 0.001 HIS D1400 PHE 0.015 0.003 PHE C1238 TYR 0.026 0.003 TYR A 683 ARG 0.003 0.001 ARG A 546 *********************** 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 fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.708 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: 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: 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: 0.6055 time to fit residues: 174.2889 Evaluate side-chains 95 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 B 821 ASN B 856 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9775 Z= 0.167 Angle : 0.551 5.739 13111 Z= 0.304 Chirality : 0.033 0.138 1476 Planarity : 0.003 0.041 1647 Dihedral : 4.198 23.480 1231 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.82 % Allowed : 7.25 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1139 helix: 1.62 (0.17), residues: 901 sheet: None (None), residues: 0 loop : -0.10 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 896 PHE 0.012 0.001 PHE C1014 TYR 0.021 0.001 TYR D1455 ARG 0.001 0.000 ARG A 395 *********************** 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 115 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.585 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: A 26 GLN cc_start: 0.9282 (tt0) cc_final: 0.9018 (tp40) REVERT: A 37 ASP cc_start: 0.9256 (t0) cc_final: 0.8605 (m-30) REVERT: A 253 MET cc_start: 0.9058 (mtp) cc_final: 0.8825 (mtp) REVERT: A 662 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7626 (tm-30) REVERT: B 846 ASP cc_start: 0.5930 (t0) cc_final: 0.5615 (t0) REVERT: C 1053 LEU cc_start: 0.8604 (tt) cc_final: 0.8340 (mt) REVERT: C 1078 ASP cc_start: 0.8918 (m-30) cc_final: 0.8636 (m-30) outliers start: 9 outliers final: 5 residues processed: 113 average time/residue: 0.5722 time to fit residues: 88.4067 Evaluate side-chains 83 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1081 GLN 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 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 709 GLN B 821 ASN D1400 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9775 Z= 0.166 Angle : 0.498 7.441 13111 Z= 0.275 Chirality : 0.032 0.137 1476 Planarity : 0.003 0.038 1647 Dihedral : 3.997 30.881 1231 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.82 % Allowed : 7.88 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.24), residues: 1139 helix: 2.02 (0.17), residues: 904 sheet: None (None), residues: 0 loop : -0.11 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 889 PHE 0.011 0.001 PHE D1499 TYR 0.015 0.001 TYR D1455 ARG 0.002 0.000 ARG A 240 *********************** 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 90 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.665 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: A 26 GLN cc_start: 0.9271 (tt0) cc_final: 0.8999 (tp40) REVERT: A 37 ASP cc_start: 0.9236 (t0) cc_final: 0.8619 (m-30) REVERT: A 662 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7840 (tm-30) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.5211 time to fit residues: 66.1128 Evaluate side-chains 81 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 903 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain D residue 1443 GLU Chi-restraints excluded: chain D residue 1452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9775 Z= 0.170 Angle : 0.471 5.204 13111 Z= 0.262 Chirality : 0.032 0.155 1476 Planarity : 0.003 0.061 1647 Dihedral : 3.790 32.868 1231 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.09 % Allowed : 7.97 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.24), residues: 1139 helix: 2.40 (0.17), residues: 909 sheet: None (None), residues: 0 loop : -0.07 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 889 PHE 0.009 0.001 PHE D1499 TYR 0.011 0.001 TYR D1455 ARG 0.002 0.000 ARG A 240 *********************** 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 92 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.633 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 26 GLN cc_start: 0.9299 (tt0) cc_final: 0.9006 (tp40) REVERT: A 37 ASP cc_start: 0.9236 (t0) cc_final: 0.8633 (m-30) REVERT: A 662 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7820 (tm-30) outliers start: 12 outliers final: 11 residues processed: 89 average time/residue: 0.5348 time to fit residues: 66.1614 Evaluate side-chains 79 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU 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 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 1507 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN C 981 ASN C1025 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9775 Z= 0.177 Angle : 0.469 5.990 13111 Z= 0.261 Chirality : 0.031 0.142 1476 Planarity : 0.003 0.049 1647 Dihedral : 3.690 35.752 1231 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.00 % Allowed : 8.42 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.24), residues: 1139 helix: 2.59 (0.16), residues: 914 sheet: None (None), residues: 0 loop : 0.01 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 22 PHE 0.009 0.001 PHE D1496 TYR 0.012 0.001 TYR D1455 ARG 0.002 0.000 ARG D1384 *********************** 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 83 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.549 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: A 26 GLN cc_start: 0.9330 (tt0) cc_final: 0.9082 (tp40) REVERT: A 37 ASP cc_start: 0.9227 (t0) cc_final: 0.8599 (m-30) REVERT: A 662 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7881 (tm-30) REVERT: B 884 MET cc_start: 0.8556 (tpp) cc_final: 0.8328 (ttm) REVERT: D 1496 PHE cc_start: 0.7899 (m-80) cc_final: 0.7558 (m-80) outliers start: 11 outliers final: 11 residues processed: 80 average time/residue: 0.5129 time to fit residues: 57.5677 Evaluate side-chains 74 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 705 LEU 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 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 100 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 ASN C1183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9775 Z= 0.187 Angle : 0.467 6.322 13111 Z= 0.260 Chirality : 0.031 0.154 1476 Planarity : 0.003 0.052 1647 Dihedral : 3.605 33.745 1231 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.18 % Allowed : 9.42 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.24), residues: 1139 helix: 2.71 (0.16), residues: 915 sheet: None (None), residues: 0 loop : 0.02 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 22 PHE 0.008 0.001 PHE D1496 TYR 0.017 0.001 TYR D1455 ARG 0.002 0.000 ARG A 577 *********************** 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 78 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 1.337 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 26 GLN cc_start: 0.9351 (tt0) cc_final: 0.9067 (tp40) REVERT: A 37 ASP cc_start: 0.9238 (t0) cc_final: 0.8601 (m-30) REVERT: A 662 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 884 MET cc_start: 0.8546 (tpp) cc_final: 0.8220 (ttm) outliers start: 13 outliers final: 11 residues processed: 75 average time/residue: 0.5211 time to fit residues: 55.2786 Evaluate side-chains 72 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 705 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9775 Z= 0.135 Angle : 0.445 6.509 13111 Z= 0.241 Chirality : 0.031 0.146 1476 Planarity : 0.003 0.055 1647 Dihedral : 3.511 32.364 1231 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.09 % Allowed : 9.60 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.25), residues: 1139 helix: 2.95 (0.17), residues: 915 sheet: None (None), residues: 0 loop : 0.08 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 168 PHE 0.006 0.001 PHE D1440 TYR 0.013 0.001 TYR C1013 ARG 0.002 0.000 ARG D1384 *********************** 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 78 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.557 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: A 26 GLN cc_start: 0.9346 (tt0) cc_final: 0.9067 (tp40) REVERT: A 37 ASP cc_start: 0.9235 (t0) cc_final: 0.8599 (m-30) REVERT: A 662 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 884 MET cc_start: 0.8511 (tpp) cc_final: 0.8099 (ttm) outliers start: 12 outliers final: 11 residues processed: 76 average time/residue: 0.4732 time to fit residues: 52.1881 Evaluate side-chains 70 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9775 Z= 0.222 Angle : 0.488 6.463 13111 Z= 0.272 Chirality : 0.032 0.141 1476 Planarity : 0.003 0.055 1647 Dihedral : 3.509 29.826 1231 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.36 % Allowed : 9.78 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.24), residues: 1139 helix: 2.85 (0.16), residues: 921 sheet: None (None), residues: 0 loop : -0.05 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 168 PHE 0.008 0.001 PHE D1496 TYR 0.014 0.001 TYR D1455 ARG 0.002 0.000 ARG A 470 *********************** 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 74 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 1.622 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 26 GLN cc_start: 0.9348 (tt0) cc_final: 0.9069 (tp40) REVERT: A 662 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 884 MET cc_start: 0.8585 (tpp) cc_final: 0.8135 (ttm) outliers start: 15 outliers final: 11 residues processed: 72 average time/residue: 0.4535 time to fit residues: 48.6439 Evaluate side-chains 69 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 705 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9775 Z= 0.136 Angle : 0.451 6.751 13111 Z= 0.243 Chirality : 0.031 0.132 1476 Planarity : 0.003 0.056 1647 Dihedral : 3.457 28.881 1231 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.18 % Allowed : 10.14 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.25), residues: 1139 helix: 3.06 (0.16), residues: 921 sheet: None (None), residues: 0 loop : 0.12 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 22 PHE 0.006 0.001 PHE D1440 TYR 0.018 0.001 TYR D1455 ARG 0.002 0.000 ARG D1384 *********************** 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 71 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 1.532 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 26 GLN cc_start: 0.9328 (tt0) cc_final: 0.9040 (tp40) REVERT: A 37 ASP cc_start: 0.9303 (t0) cc_final: 0.8701 (m-30) REVERT: A 253 MET cc_start: 0.9334 (mtp) cc_final: 0.9125 (mpp) REVERT: A 662 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 884 MET cc_start: 0.8529 (tpp) cc_final: 0.8085 (ttm) outliers start: 13 outliers final: 11 residues processed: 70 average time/residue: 0.4413 time to fit residues: 45.3856 Evaluate side-chains 69 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU 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 66 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9775 Z= 0.223 Angle : 0.483 6.411 13111 Z= 0.270 Chirality : 0.032 0.160 1476 Planarity : 0.003 0.055 1647 Dihedral : 3.435 22.230 1231 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.09 % Allowed : 10.05 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.24), residues: 1139 helix: 2.91 (0.16), residues: 921 sheet: None (None), residues: 0 loop : -0.23 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 22 PHE 0.008 0.001 PHE D1496 TYR 0.019 0.001 TYR D1455 ARG 0.002 0.001 ARG A 652 ********************** 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 70 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 1.809 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 26 GLN cc_start: 0.9360 (tt0) cc_final: 0.9087 (tp40) REVERT: A 37 ASP cc_start: 0.9324 (t0) cc_final: 0.8671 (m-30) REVERT: A 253 MET cc_start: 0.9345 (mtp) cc_final: 0.9107 (mpp) REVERT: A 662 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 884 MET cc_start: 0.8596 (tpp) cc_final: 0.8143 (ttm) outliers start: 12 outliers final: 11 residues processed: 69 average time/residue: 0.4605 time to fit residues: 47.2664 Evaluate side-chains 68 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 705 LEU 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 27 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 GLN C1097 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.055864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.046197 restraints weight = 188760.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.047995 restraints weight = 83743.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.049122 restraints weight = 49778.348| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9775 Z= 0.137 Angle : 0.454 6.694 13111 Z= 0.246 Chirality : 0.031 0.131 1476 Planarity : 0.003 0.054 1647 Dihedral : 3.565 46.295 1231 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.09 % Allowed : 10.33 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.25), residues: 1139 helix: 3.12 (0.16), residues: 919 sheet: None (None), residues: 0 loop : -0.02 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 22 PHE 0.007 0.001 PHE D1440 TYR 0.021 0.001 TYR D1455 ARG 0.002 0.000 ARG D1384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3630.78 seconds wall clock time: 65 minutes 15.38 seconds (3915.38 seconds total)