Starting phenix.real_space_refine on Thu Mar 14 18:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zka_14760/03_2024/7zka_14760.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zka_14760/03_2024/7zka_14760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zka_14760/03_2024/7zka_14760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zka_14760/03_2024/7zka_14760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zka_14760/03_2024/7zka_14760.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zka_14760/03_2024/7zka_14760.pdb" } resolution = 2.9 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 6053 2.51 5 N 1566 2.21 5 O 1743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A GLU 1096": "OE1" <-> "OE2" 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: 9406 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9406 Unusual residues: {' MG': 2, 'ATP': 2, 'JIZ': 1, 'LMN': 1, 'Y01': 3} Classifications: {'peptide': 1177, 'undetermined': 9, 'water': 4} Link IDs: {'PTRANS': 29, 'TRANS': 1147, None: 13} Not linked: pdbres="ALA A1271 " pdbres="JIZ A1401 " Not linked: pdbres="JIZ A1401 " pdbres="ATP A1402 " Not linked: pdbres="ATP A1402 " pdbres=" MG A1403 " Not linked: pdbres=" MG A1403 " pdbres="ATP A1404 " Not linked: pdbres="ATP A1404 " pdbres=" MG A1405 " ... (remaining 8 not shown) Chain breaks: 1 Time building chain proxies: 5.77, per 1000 atoms: 0.61 Number of scatterers: 9406 At special positions: 0 Unit cell: (71.625, 85.377, 150.699, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1743 8.00 N 1566 7.00 C 6053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.4 seconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 71.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 43 through 72 removed outlier: 4.269A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 94 through 154 removed outlier: 3.565A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.236A pdb=" N ASN A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 216 removed outlier: 3.910A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LYS A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 256 removed outlier: 3.707A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 265 through 319 removed outlier: 3.753A pdb=" N ASN A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 366 removed outlier: 4.473A pdb=" N ILE A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 3.857A pdb=" N TYR A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 542 Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.596A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 3.739A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.620A pdb=" N LEU A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 703 through 737 removed outlier: 3.753A pdb=" N PHE A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 749 through 795 Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.562A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 824 Processing helix chain 'A' and resid 828 through 850 Processing helix chain 'A' and resid 853 through 899 removed outlier: 3.588A pdb=" N LEU A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 3.777A pdb=" N LEU A 880 " --> pdb=" O SER A 876 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS A 881 " --> pdb=" O GLY A 877 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 907 Processing helix chain 'A' and resid 908 through 962 removed outlier: 4.537A pdb=" N ILE A 922 " --> pdb=" O GLN A 918 " (cutoff:3.500A) Proline residue: A 923 - end of helix Processing helix chain 'A' and resid 969 through 1010 Proline residue: A 992 - end of helix removed outlier: 3.956A pdb=" N VAL A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.617A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1108 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1157 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 4.099A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1217 removed outlier: 3.587A pdb=" N ALA A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1236 Processing helix chain 'A' and resid 1252 through 1259 removed outlier: 3.505A pdb=" N GLN A1259 " --> pdb=" O GLN A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1271 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 412 removed outlier: 6.789A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE A 390 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER A 448 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN A 392 " --> pdb=" O MET A 446 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N MET A 446 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.444A pdb=" N GLY A 467 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP A 551 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 469 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 548 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 581 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 550 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 594 " --> pdb=" O GLN A 605 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 605 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY A 596 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1050 through 1056 removed outlier: 6.881A pdb=" N GLN A1050 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A1037 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU A1052 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE A1033 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A1091 " --> pdb=" O PHE A1033 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY A1035 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER A1089 " --> pdb=" O GLY A1035 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.379A pdb=" N GLY A1110 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP A1196 " --> pdb=" O GLY A1110 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A1112 " --> pdb=" O ASP A1196 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A1062 " --> pdb=" O VAL A1225 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A1239 " --> pdb=" O HIS A1250 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS A1250 " --> pdb=" O ILE A1239 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A1241 " --> pdb=" O LYS A1248 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1845 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: 3.01 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1514 1.31 - 1.44: 2466 1.44 - 1.56: 5509 1.56 - 1.69: 34 1.69 - 1.82: 64 Bond restraints: 9587 Sorted by residual: bond pdb=" C03 JIZ A1401 " pdb=" N02 JIZ A1401 " ideal model delta sigma weight residual 1.367 1.639 -0.272 2.00e-02 2.50e+03 1.86e+02 bond pdb=" C08 JIZ A1401 " pdb=" N04 JIZ A1401 " ideal model delta sigma weight residual 1.366 1.616 -0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C13 JIZ A1401 " pdb=" N06 JIZ A1401 " ideal model delta sigma weight residual 1.366 1.615 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C02 JIZ A1401 " pdb=" S01 JIZ A1401 " ideal model delta sigma weight residual 1.728 1.546 0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" C03 JIZ A1401 " pdb=" C04 JIZ A1401 " ideal model delta sigma weight residual 1.360 1.520 -0.160 2.00e-02 2.50e+03 6.39e+01 ... (remaining 9582 not shown) Histogram of bond angle deviations from ideal: 98.55 - 106.82: 237 106.82 - 115.09: 5914 115.09 - 123.36: 6516 123.36 - 131.63: 310 131.63 - 139.90: 17 Bond angle restraints: 12994 Sorted by residual: angle pdb=" N ILE A 318 " pdb=" CA ILE A 318 " pdb=" C ILE A 318 " ideal model delta sigma weight residual 111.90 99.57 12.33 8.10e-01 1.52e+00 2.32e+02 angle pdb=" N PRO A 741 " pdb=" CA PRO A 741 " pdb=" C PRO A 741 " ideal model delta sigma weight residual 113.47 131.27 -17.80 1.43e+00 4.89e-01 1.55e+02 angle pdb=" N GLN A 746 " pdb=" CA GLN A 746 " pdb=" C GLN A 746 " ideal model delta sigma weight residual 111.28 103.00 8.28 1.09e+00 8.42e-01 5.77e+01 angle pdb=" N PRO A 740 " pdb=" CA PRO A 740 " pdb=" C PRO A 740 " ideal model delta sigma weight residual 110.70 102.31 8.39 1.22e+00 6.72e-01 4.73e+01 angle pdb=" N LYS A 86 " pdb=" CA LYS A 86 " pdb=" C LYS A 86 " ideal model delta sigma weight residual 112.57 105.01 7.56 1.13e+00 7.83e-01 4.47e+01 ... (remaining 12989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 5499 24.39 - 48.78: 363 48.78 - 73.17: 70 73.17 - 97.56: 27 97.56 - 121.95: 22 Dihedral angle restraints: 5981 sinusoidal: 2610 harmonic: 3371 Sorted by residual: dihedral pdb=" C LEU A 519 " pdb=" N LEU A 519 " pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " ideal model delta harmonic sigma weight residual -122.60 -137.47 14.87 0 2.50e+00 1.60e-01 3.54e+01 dihedral pdb=" N LEU A 519 " pdb=" C LEU A 519 " pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " ideal model delta harmonic sigma weight residual 122.80 135.32 -12.52 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C PHE A 516 " pdb=" N PHE A 516 " pdb=" CA PHE A 516 " pdb=" CB PHE A 516 " ideal model delta harmonic sigma weight residual -122.60 -112.15 -10.45 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 5978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1458 0.131 - 0.261: 33 0.261 - 0.392: 7 0.392 - 0.523: 2 0.523 - 0.653: 1 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA PRO A 741 " pdb=" N PRO A 741 " pdb=" C PRO A 741 " pdb=" CB PRO A 741 " both_signs ideal model delta sigma weight residual False 2.72 2.06 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA LEU A 519 " pdb=" N LEU A 519 " pdb=" C LEU A 519 " pdb=" CB LEU A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 1498 not shown) Planarity restraints: 1613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 736 " -0.016 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C THR A 736 " 0.059 2.00e-02 2.50e+03 pdb=" O THR A 736 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 737 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 218 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO A 219 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 520 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C VAL A 520 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL A 520 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY A 521 " -0.016 2.00e-02 2.50e+03 ... (remaining 1610 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 95 2.61 - 3.18: 8453 3.18 - 3.75: 15131 3.75 - 4.33: 21212 4.33 - 4.90: 34202 Nonbonded interactions: 79093 Sorted by model distance: nonbonded pdb=" OG SER A1073 " pdb="MG MG A1405 " model vdw 2.034 2.170 nonbonded pdb=" O2G ATP A1404 " pdb="MG MG A1405 " model vdw 2.049 2.170 nonbonded pdb=" OG SER A 430 " pdb="MG MG A1403 " model vdw 2.063 2.170 nonbonded pdb=" OE1 GLN A1114 " pdb="MG MG A1405 " model vdw 2.066 2.170 nonbonded pdb=" O2B ATP A1404 " pdb="MG MG A1405 " model vdw 2.075 2.170 ... (remaining 79088 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.550 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 26.320 Find NCS groups from input model: 0.220 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 : 0.009 0.272 9587 Z= 0.588 Angle : 0.871 17.803 12994 Z= 0.522 Chirality : 0.057 0.653 1501 Planarity : 0.005 0.079 1613 Dihedral : 19.022 121.954 3821 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.19 % 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: 1.13 (0.24), residues: 1173 helix: 1.40 (0.18), residues: 795 sheet: -0.40 (0.61), residues: 70 loop : -0.55 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.003 0.001 HIS A 932 PHE 0.025 0.001 PHE A 953 TYR 0.010 0.001 TYR A 440 ARG 0.003 0.000 ARG A 925 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.030 Fit side-chains REVERT: A 193 MET cc_start: 0.6753 (mmp) cc_final: 0.6482 (mmp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 1.2378 time to fit residues: 191.8990 Evaluate side-chains 105 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 93 optimal weight: 0.0270 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 515 GLN A 749 ASN A 835 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9587 Z= 0.167 Angle : 0.574 9.878 12994 Z= 0.284 Chirality : 0.043 0.248 1501 Planarity : 0.004 0.065 1613 Dihedral : 14.574 98.510 1702 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 1.76 % Allowed : 9.83 % Favored : 88.41 % 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: 1.67 (0.24), residues: 1173 helix: 1.81 (0.18), residues: 800 sheet: 0.01 (0.62), residues: 70 loop : -0.47 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 311 HIS 0.005 0.001 HIS A 608 PHE 0.022 0.001 PHE A 508 TYR 0.008 0.001 TYR A 440 ARG 0.004 0.000 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.033 Fit side-chains outliers start: 17 outliers final: 4 residues processed: 118 average time/residue: 1.3253 time to fit residues: 167.0798 Evaluate side-chains 104 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 965 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9587 Z= 0.196 Angle : 0.545 7.868 12994 Z= 0.273 Chirality : 0.042 0.316 1501 Planarity : 0.004 0.063 1613 Dihedral : 11.833 85.530 1702 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.53 % Rotamer: Outliers : 2.17 % Allowed : 12.01 % Favored : 85.82 % 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: 1.77 (0.24), residues: 1173 helix: 1.92 (0.18), residues: 801 sheet: 0.14 (0.62), residues: 70 loop : -0.54 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 158 HIS 0.005 0.001 HIS A 608 PHE 0.020 0.001 PHE A 619 TYR 0.009 0.001 TYR A 306 ARG 0.004 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6212 (mpp) REVERT: A 1189 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7442 (mt0) outliers start: 21 outliers final: 11 residues processed: 111 average time/residue: 1.2908 time to fit residues: 153.3114 Evaluate side-chains 111 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 394 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9587 Z= 0.209 Angle : 0.525 7.159 12994 Z= 0.267 Chirality : 0.041 0.192 1501 Planarity : 0.004 0.061 1613 Dihedral : 10.253 85.023 1702 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 2.69 % Allowed : 13.66 % Favored : 83.64 % 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: 1.75 (0.24), residues: 1173 helix: 1.92 (0.18), residues: 805 sheet: 0.07 (0.61), residues: 70 loop : -0.66 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 158 HIS 0.004 0.001 HIS A 608 PHE 0.019 0.001 PHE A 508 TYR 0.010 0.001 TYR A 306 ARG 0.004 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6185 (mpp) REVERT: A 940 PHE cc_start: 0.6988 (t80) cc_final: 0.6721 (t80) REVERT: A 1189 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7448 (mt0) outliers start: 26 outliers final: 11 residues processed: 122 average time/residue: 1.3112 time to fit residues: 171.0119 Evaluate side-chains 117 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 139 GLN A 394 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9587 Z= 0.222 Angle : 0.523 7.335 12994 Z= 0.269 Chirality : 0.041 0.179 1501 Planarity : 0.004 0.061 1613 Dihedral : 9.850 83.321 1702 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.21 % Allowed : 14.60 % Favored : 82.19 % 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: 1.74 (0.24), residues: 1173 helix: 1.91 (0.18), residues: 806 sheet: 0.11 (0.62), residues: 70 loop : -0.67 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 158 HIS 0.005 0.001 HIS A 608 PHE 0.020 0.001 PHE A 508 TYR 0.010 0.001 TYR A 306 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6194 (mpp) REVERT: A 1009 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: A 1189 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7481 (mt0) outliers start: 31 outliers final: 13 residues processed: 129 average time/residue: 1.2600 time to fit residues: 174.0757 Evaluate side-chains 117 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 0.0570 chunk 111 optimal weight: 4.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 394 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9587 Z= 0.240 Angle : 0.537 7.473 12994 Z= 0.275 Chirality : 0.041 0.189 1501 Planarity : 0.004 0.061 1613 Dihedral : 9.768 84.088 1702 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.69 % Allowed : 16.36 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.75 (0.24), residues: 1173 helix: 1.91 (0.18), residues: 806 sheet: 0.06 (0.62), residues: 70 loop : -0.61 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 158 HIS 0.006 0.001 HIS A 514 PHE 0.024 0.001 PHE A 619 TYR 0.010 0.001 TYR A 306 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.881 Fit side-chains REVERT: A 188 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6499 (mpp) REVERT: A 1009 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: A 1189 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7492 (mt0) outliers start: 26 outliers final: 14 residues processed: 119 average time/residue: 1.3238 time to fit residues: 168.5935 Evaluate side-chains 119 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 71 optimal weight: 0.0070 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 394 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9587 Z= 0.157 Angle : 0.486 7.223 12994 Z= 0.252 Chirality : 0.039 0.233 1501 Planarity : 0.004 0.061 1613 Dihedral : 9.480 80.201 1702 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.17 % Allowed : 17.49 % Favored : 80.33 % 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: 1.96 (0.25), residues: 1173 helix: 2.09 (0.18), residues: 805 sheet: 0.06 (0.62), residues: 70 loop : -0.59 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 704 HIS 0.004 0.001 HIS A 608 PHE 0.016 0.001 PHE A 508 TYR 0.010 0.001 TYR A 306 ARG 0.004 0.000 ARG A 925 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.887 Fit side-chains REVERT: A 188 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6293 (mpp) REVERT: A 1009 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6224 (mp0) outliers start: 21 outliers final: 9 residues processed: 116 average time/residue: 1.2374 time to fit residues: 153.7480 Evaluate side-chains 111 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9587 Z= 0.222 Angle : 0.516 7.253 12994 Z= 0.267 Chirality : 0.040 0.204 1501 Planarity : 0.004 0.061 1613 Dihedral : 9.594 81.870 1702 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.86 % Allowed : 17.91 % Favored : 80.23 % 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: 1.84 (0.24), residues: 1173 helix: 2.01 (0.18), residues: 807 sheet: -0.07 (0.62), residues: 73 loop : -0.65 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 158 HIS 0.005 0.001 HIS A 608 PHE 0.019 0.001 PHE A 508 TYR 0.011 0.001 TYR A 306 ARG 0.004 0.000 ARG A 925 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.989 Fit side-chains REVERT: A 188 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6479 (mpp) REVERT: A 295 MET cc_start: 0.7795 (ttt) cc_final: 0.7532 (ttt) REVERT: A 1009 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6221 (mp0) outliers start: 18 outliers final: 9 residues processed: 114 average time/residue: 1.3617 time to fit residues: 165.6791 Evaluate side-chains 111 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.0270 chunk 101 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9587 Z= 0.182 Angle : 0.493 7.195 12994 Z= 0.256 Chirality : 0.040 0.216 1501 Planarity : 0.004 0.061 1613 Dihedral : 9.502 81.800 1702 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.97 % Allowed : 17.81 % Favored : 80.23 % 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: 1.92 (0.25), residues: 1173 helix: 2.07 (0.18), residues: 805 sheet: -0.05 (0.62), residues: 73 loop : -0.61 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 704 HIS 0.004 0.001 HIS A 608 PHE 0.018 0.001 PHE A 508 TYR 0.011 0.001 TYR A 306 ARG 0.004 0.000 ARG A 925 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.081 Fit side-chains REVERT: A 188 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6446 (mpp) REVERT: A 295 MET cc_start: 0.7784 (ttt) cc_final: 0.7529 (ttt) REVERT: A 953 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6469 (t80) REVERT: A 1009 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: A 1189 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7490 (mt0) outliers start: 19 outliers final: 10 residues processed: 108 average time/residue: 1.3759 time to fit residues: 158.6236 Evaluate side-chains 113 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 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 963 GLN A1211 GLN A1250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9587 Z= 0.275 Angle : 0.547 7.950 12994 Z= 0.282 Chirality : 0.042 0.212 1501 Planarity : 0.004 0.062 1613 Dihedral : 9.763 84.757 1702 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.17 % Allowed : 17.60 % Favored : 80.23 % 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: 1.74 (0.24), residues: 1173 helix: 1.93 (0.18), residues: 806 sheet: -0.13 (0.61), residues: 73 loop : -0.64 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 158 HIS 0.004 0.001 HIS A 608 PHE 0.023 0.002 PHE A 508 TYR 0.011 0.001 TYR A 306 ARG 0.005 0.000 ARG A 925 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.032 Fit side-chains REVERT: A 188 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6614 (mpp) REVERT: A 1009 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: A 1189 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7506 (mt0) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 1.3518 time to fit residues: 161.5436 Evaluate side-chains 117 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 68 optimal weight: 0.6980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124831 restraints weight = 10210.703| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.71 r_work: 0.3138 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9587 Z= 0.150 Angle : 0.497 10.895 12994 Z= 0.255 Chirality : 0.039 0.227 1501 Planarity : 0.004 0.061 1613 Dihedral : 9.467 82.798 1702 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.35 % Allowed : 18.32 % Favored : 80.33 % 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: 1.96 (0.25), residues: 1173 helix: 2.12 (0.18), residues: 805 sheet: -0.12 (0.62), residues: 73 loop : -0.63 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1104 HIS 0.003 0.001 HIS A 608 PHE 0.015 0.001 PHE A 508 TYR 0.011 0.001 TYR A 306 ARG 0.004 0.000 ARG A 925 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3892.14 seconds wall clock time: 69 minutes 16.65 seconds (4156.65 seconds total)