Starting phenix.real_space_refine on Mon Aug 5 01:00:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/08_2024/8w41_37260.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/08_2024/8w41_37260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/08_2024/8w41_37260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/08_2024/8w41_37260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/08_2024/8w41_37260.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/08_2024/8w41_37260.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 28 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 68 5.16 5 C 7417 2.51 5 N 2071 2.21 5 O 2295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 48": "OE1" <-> "OE2" Residue "I GLU 8": "OE1" <-> "OE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "A ARG 825": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A ARG 939": "NH1" <-> "NH2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A GLU 986": "OE1" <-> "OE2" Residue "A GLU 1004": "OE1" <-> "OE2" Residue "A ARG 1007": "NH1" <-> "NH2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A TYR 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A ARG 1172": "NH1" <-> "NH2" Residue "A ARG 1177": "NH1" <-> "NH2" Residue "A ARG 1204": "NH1" <-> "NH2" Residue "A GLU 1232": "OE1" <-> "OE2" Residue "A ARG 1240": "NH1" <-> "NH2" Residue "A GLU 1254": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11859 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1156 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "I" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "A" Number of atoms: 9515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 9515 Classifications: {'peptide': 1162} Link IDs: {'PTRANS': 37, 'TRANS': 1124} Chain breaks: 4 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.42, per 1000 atoms: 0.71 Number of scatterers: 11859 At special positions: 0 Unit cell: (74.43, 102.548, 186.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 68 16.00 P 3 15.00 Mg 1 11.99 O 2295 8.00 N 2071 7.00 C 7417 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=0, symmetry=0 Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 2.2 seconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 8 sheets defined 63.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'B' and resid 6 through 21 Processing helix chain 'B' and resid 29 through 40 removed outlier: 4.096A pdb=" N LEU B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.562A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.661A pdb=" N ASP B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'I' and resid 6 through 20 Processing helix chain 'I' and resid 29 through 38 removed outlier: 4.180A pdb=" N THR I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 57 Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 65 through 79 removed outlier: 4.046A pdb=" N ASP I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 93 removed outlier: 4.003A pdb=" N PHE I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 113 Processing helix chain 'I' and resid 118 through 129 removed outlier: 3.710A pdb=" N VAL I 122 " --> pdb=" O THR I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 148 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.520A pdb=" N SER A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.517A pdb=" N TYR A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 removed outlier: 3.504A pdb=" N ILE A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.566A pdb=" N ASN A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.761A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.883A pdb=" N CYS A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.077A pdb=" N ARG A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.665A pdb=" N GLY A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 350 " --> pdb=" O HIS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 379 removed outlier: 4.445A pdb=" N GLN A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 392 removed outlier: 3.583A pdb=" N THR A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 443 removed outlier: 3.769A pdb=" N PHE A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 489 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 511 through 520 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 539 through 551 Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.549A pdb=" N GLU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 642 through 661 Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.518A pdb=" N ILE A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 711 through 720 removed outlier: 3.879A pdb=" N LYS A 720 " --> pdb=" O ASN A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.666A pdb=" N ARG A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 removed outlier: 3.561A pdb=" N PHE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 3.750A pdb=" N GLN A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 829 removed outlier: 3.994A pdb=" N VAL A 796 " --> pdb=" O ARG A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 860 removed outlier: 3.982A pdb=" N GLU A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 888 removed outlier: 3.709A pdb=" N MET A 867 " --> pdb=" O GLY A 863 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 920 removed outlier: 3.558A pdb=" N LYS A 904 " --> pdb=" O ASP A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 979 removed outlier: 3.935A pdb=" N ARG A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 963 " --> pdb=" O GLU A 959 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1021 removed outlier: 3.605A pdb=" N ARG A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 3.511A pdb=" N LEU A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1119 removed outlier: 3.630A pdb=" N ALA A1100 " --> pdb=" O GLU A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1136 Processing helix chain 'A' and resid 1177 through 1181 removed outlier: 3.888A pdb=" N GLN A1181 " --> pdb=" O PRO A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 Processing helix chain 'A' and resid 1245 through 1255 removed outlier: 3.644A pdb=" N PHE A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1268 Processing sheet with id=AA1, first strand: chain 'I' and resid 100 through 101 removed outlier: 3.530A pdb=" N VAL I 137 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.587A pdb=" N PHE A 41 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 43 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 20 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.311A pdb=" N LEU A 94 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 669 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 96 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 666 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN A 145 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU A 455 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE A 147 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 226 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA6, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AA7, first strand: chain 'A' and resid 707 through 710 removed outlier: 3.588A pdb=" N SER A 707 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1168 through 1174 removed outlier: 5.751A pdb=" N TRP A1192 " --> pdb=" O GLU A1207 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A1207 " --> pdb=" O TRP A1192 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A1194 " --> pdb=" O GLN A1205 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN A1205 " --> pdb=" O TYR A1194 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS A1196 " --> pdb=" O ALA A1203 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP A1201 " --> pdb=" O ASP A1198 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 5.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2139 1.31 - 1.44: 2999 1.44 - 1.56: 6802 1.56 - 1.69: 3 1.69 - 1.81: 112 Bond restraints: 12055 Sorted by residual: bond pdb=" CA ILE A1244 " pdb=" C ILE A1244 " ideal model delta sigma weight residual 1.526 1.415 0.111 1.16e-02 7.43e+03 9.11e+01 bond pdb=" CA MET A1224 " pdb=" C MET A1224 " ideal model delta sigma weight residual 1.523 1.430 0.093 1.34e-02 5.57e+03 4.85e+01 bond pdb=" CA GLU A 152 " pdb=" C GLU A 152 " ideal model delta sigma weight residual 1.528 1.435 0.092 1.33e-02 5.65e+03 4.83e+01 bond pdb=" CA LYS A1221 " pdb=" C LYS A1221 " ideal model delta sigma weight residual 1.530 1.469 0.060 9.10e-03 1.21e+04 4.41e+01 bond pdb=" CA GLU A1104 " pdb=" C GLU A1104 " ideal model delta sigma weight residual 1.524 1.441 0.083 1.29e-02 6.01e+03 4.16e+01 ... (remaining 12050 not shown) Histogram of bond angle deviations from ideal: 89.98 - 99.18: 10 99.18 - 108.38: 504 108.38 - 117.59: 8228 117.59 - 126.79: 7337 126.79 - 135.99: 105 Bond angle restraints: 16184 Sorted by residual: angle pdb=" N ILE A1089 " pdb=" CA ILE A1089 " pdb=" C ILE A1089 " ideal model delta sigma weight residual 113.53 94.41 19.12 9.80e-01 1.04e+00 3.81e+02 angle pdb=" N LYS A1221 " pdb=" CA LYS A1221 " pdb=" C LYS A1221 " ideal model delta sigma weight residual 108.49 89.98 18.51 1.15e+00 7.56e-01 2.59e+02 angle pdb=" N ARG A1102 " pdb=" CA ARG A1102 " pdb=" C ARG A1102 " ideal model delta sigma weight residual 111.82 101.33 10.49 1.16e+00 7.43e-01 8.17e+01 angle pdb=" N GLU I 105 " pdb=" CA GLU I 105 " pdb=" C GLU I 105 " ideal model delta sigma weight residual 111.36 102.39 8.97 1.09e+00 8.42e-01 6.77e+01 angle pdb=" N PHE A1249 " pdb=" CA PHE A1249 " pdb=" C PHE A1249 " ideal model delta sigma weight residual 111.14 102.90 8.24 1.08e+00 8.57e-01 5.82e+01 ... (remaining 16179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.25: 7170 31.25 - 62.51: 247 62.51 - 93.76: 15 93.76 - 125.01: 0 125.01 - 156.27: 3 Dihedral angle restraints: 7435 sinusoidal: 3188 harmonic: 4247 Sorted by residual: dihedral pdb=" N GLU A1103 " pdb=" C GLU A1103 " pdb=" CA GLU A1103 " pdb=" CB GLU A1103 " ideal model delta harmonic sigma weight residual 122.80 140.00 -17.20 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 96.27 -156.27 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" C GLU A1103 " pdb=" N GLU A1103 " pdb=" CA GLU A1103 " pdb=" CB GLU A1103 " ideal model delta harmonic sigma weight residual -122.60 -138.75 16.15 0 2.50e+00 1.60e-01 4.18e+01 ... (remaining 7432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1685 0.145 - 0.289: 33 0.289 - 0.434: 7 0.434 - 0.579: 0 0.579 - 0.724: 1 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA GLU A1103 " pdb=" N GLU A1103 " pdb=" C GLU A1103 " pdb=" CB GLU A1103 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ILE A1244 " pdb=" N ILE A1244 " pdb=" C ILE A1244 " pdb=" CB ILE A1244 " both_signs ideal model delta sigma weight residual False 2.43 2.04 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA GLU A1254 " pdb=" N GLU A1254 " pdb=" C GLU A1254 " pdb=" CB GLU A1254 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 1723 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 705 " -0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 706 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 706 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 706 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1082 " -0.033 2.00e-02 2.50e+03 2.08e-02 8.66e+00 pdb=" CG TYR A1082 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A1082 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A1082 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1082 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A1082 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1082 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A1082 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1212 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A1213 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A1213 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1213 " 0.035 5.00e-02 4.00e+02 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 129 2.51 - 3.11: 9509 3.11 - 3.71: 19529 3.71 - 4.30: 26689 4.30 - 4.90: 42974 Nonbonded interactions: 98830 Sorted by model distance: nonbonded pdb=" O1B ADP A2001 " pdb="MG MG A2002 " model vdw 1.918 2.170 nonbonded pdb="MG MG A2002 " pdb=" O2 PO4 A2003 " model vdw 1.976 2.170 nonbonded pdb=" OG SER A 204 " pdb="MG MG A2002 " model vdw 2.008 2.170 nonbonded pdb=" N LYS A1221 " pdb=" O LYS A1221 " model vdw 2.105 2.496 nonbonded pdb=" O LEU A1231 " pdb=" OG1 THR A1234 " model vdw 2.127 3.040 ... (remaining 98825 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 3 through 148) selection = chain 'I' } 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.530 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 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 : 0.008 0.111 12055 Z= 0.513 Angle : 0.912 19.118 16184 Z= 0.565 Chirality : 0.060 0.724 1726 Planarity : 0.005 0.096 2127 Dihedral : 15.405 156.268 4677 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.63 % Allowed : 1.32 % Favored : 97.05 % Cbeta Deviations : 0.15 % 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: -1.05 (0.21), residues: 1441 helix: -0.00 (0.17), residues: 837 sheet: -2.39 (0.47), residues: 107 loop : -1.32 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A1253 HIS 0.009 0.001 HIS A 833 PHE 0.039 0.003 PHE I 66 TYR 0.047 0.002 TYR A1082 ARG 0.022 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 311 time to evaluate : 1.239 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: B 77 MET cc_start: 0.6807 (pmm) cc_final: 0.6389 (pmm) REVERT: B 83 GLU cc_start: 0.7060 (tp30) cc_final: 0.6599 (tp30) REVERT: I 38 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6616 (ttm110) REVERT: I 42 GLN cc_start: 0.5856 (pp30) cc_final: 0.5120 (pp30) REVERT: I 50 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6981 (tm-30) REVERT: I 72 MET cc_start: 0.7568 (mmp) cc_final: 0.7363 (mmp) REVERT: I 73 MET cc_start: 0.7331 (tpt) cc_final: 0.6782 (tpt) REVERT: I 108 HIS cc_start: 0.7393 (m170) cc_final: 0.7191 (m170) REVERT: I 124 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7247 (mm-30) REVERT: I 141 GLU cc_start: 0.4241 (mm-30) cc_final: 0.3843 (mm-30) REVERT: A 5 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8251 (ptpp) REVERT: A 46 ASN cc_start: 0.7613 (p0) cc_final: 0.7408 (p0) REVERT: A 132 ASP cc_start: 0.6276 (t70) cc_final: 0.5795 (t0) REVERT: A 135 PHE cc_start: 0.7674 (t80) cc_final: 0.7359 (t80) REVERT: A 138 MET cc_start: 0.7230 (tmm) cc_final: 0.6970 (tmm) REVERT: A 176 GLN cc_start: 0.7550 (pm20) cc_final: 0.7230 (pm20) REVERT: A 180 ASP cc_start: 0.7355 (m-30) cc_final: 0.7017 (m-30) REVERT: A 196 LYS cc_start: 0.8249 (tttm) cc_final: 0.7905 (tttm) REVERT: A 264 HIS cc_start: 0.7727 (m170) cc_final: 0.7376 (m170) REVERT: A 327 ILE cc_start: 0.7967 (pt) cc_final: 0.7226 (pt) REVERT: A 377 GLU cc_start: 0.7785 (tt0) cc_final: 0.7583 (tt0) REVERT: A 387 ARG cc_start: 0.7443 (pmt170) cc_final: 0.6936 (pmt170) REVERT: A 491 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 575 GLU cc_start: 0.6287 (mp0) cc_final: 0.6029 (mp0) REVERT: A 596 LYS cc_start: 0.8142 (mptt) cc_final: 0.7883 (mptt) REVERT: A 609 ILE cc_start: 0.8229 (tp) cc_final: 0.7966 (tp) REVERT: A 611 GLU cc_start: 0.6973 (mp0) cc_final: 0.6766 (mp0) REVERT: A 617 ILE cc_start: 0.8336 (mm) cc_final: 0.8065 (mm) REVERT: A 619 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6555 (mt-10) REVERT: A 701 MET cc_start: 0.7078 (mmt) cc_final: 0.6789 (mmt) REVERT: A 732 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7778 (ttp80) REVERT: A 765 GLU cc_start: 0.6707 (mp0) cc_final: 0.6396 (mp0) REVERT: A 799 CYS cc_start: 0.6902 (t) cc_final: 0.6629 (t) REVERT: A 802 SER cc_start: 0.7427 (t) cc_final: 0.7073 (p) REVERT: A 956 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7416 (tmm) REVERT: A 959 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: A 961 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: A 1104 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7577 (mm-30) REVERT: A 1105 PHE cc_start: 0.8186 (t80) cc_final: 0.7926 (t80) REVERT: A 1193 TRP cc_start: 0.8375 (t60) cc_final: 0.8087 (t60) REVERT: A 1223 ASP cc_start: 0.7276 (t0) cc_final: 0.6716 (t0) outliers start: 21 outliers final: 5 residues processed: 323 average time/residue: 0.2969 time to fit residues: 129.5469 Evaluate side-chains 305 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 297 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 MET Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1222 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 0.0370 chunk 37 optimal weight: 0.4980 chunk 73 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN A 868 ASN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12055 Z= 0.208 Angle : 0.647 10.136 16184 Z= 0.342 Chirality : 0.043 0.165 1726 Planarity : 0.005 0.063 2127 Dihedral : 8.909 152.757 1611 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 1.94 % Allowed : 8.68 % Favored : 89.38 % 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: -0.31 (0.21), residues: 1441 helix: 0.59 (0.17), residues: 851 sheet: -1.86 (0.48), residues: 112 loop : -1.08 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1253 HIS 0.003 0.001 HIS A 246 PHE 0.036 0.002 PHE A 853 TYR 0.014 0.002 TYR A 462 ARG 0.007 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 302 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8212 (mtp) cc_final: 0.7821 (mtm) REVERT: B 73 MET cc_start: 0.6548 (mmt) cc_final: 0.6205 (mmp) REVERT: B 77 MET cc_start: 0.6678 (pmm) cc_final: 0.6309 (pmm) REVERT: B 83 GLU cc_start: 0.6952 (tp30) cc_final: 0.6538 (tp30) REVERT: I 12 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7479 (tm-30) REVERT: I 50 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7233 (tm-30) REVERT: I 73 MET cc_start: 0.7186 (tpt) cc_final: 0.5780 (tpt) REVERT: I 77 MET cc_start: 0.7587 (ptp) cc_final: 0.6356 (ptp) REVERT: I 107 ARG cc_start: 0.7369 (ttt-90) cc_final: 0.7025 (ttt-90) REVERT: I 108 HIS cc_start: 0.7244 (m170) cc_final: 0.7013 (m170) REVERT: I 110 MET cc_start: 0.7177 (mpp) cc_final: 0.6932 (mpp) REVERT: I 120 GLU cc_start: 0.7350 (pm20) cc_final: 0.7030 (pm20) REVERT: I 146 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6300 (mmm) REVERT: A 16 PHE cc_start: 0.7973 (m-80) cc_final: 0.7397 (m-80) REVERT: A 24 ILE cc_start: 0.7801 (mt) cc_final: 0.7542 (mt) REVERT: A 125 PRO cc_start: 0.8365 (Cg_exo) cc_final: 0.8164 (Cg_endo) REVERT: A 146 SER cc_start: 0.8180 (p) cc_final: 0.7886 (m) REVERT: A 228 TYR cc_start: 0.8558 (m-80) cc_final: 0.7952 (m-80) REVERT: A 264 HIS cc_start: 0.7663 (m170) cc_final: 0.7391 (m170) REVERT: A 327 ILE cc_start: 0.7980 (pt) cc_final: 0.7664 (pt) REVERT: A 377 GLU cc_start: 0.7737 (tt0) cc_final: 0.7518 (tt0) REVERT: A 448 SER cc_start: 0.8238 (p) cc_final: 0.7969 (m) REVERT: A 575 GLU cc_start: 0.6218 (mp0) cc_final: 0.5830 (mp0) REVERT: A 580 ARG cc_start: 0.6746 (mpp80) cc_final: 0.6517 (mpp80) REVERT: A 603 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6863 (tpt) REVERT: A 617 ILE cc_start: 0.8439 (mm) cc_final: 0.8229 (mm) REVERT: A 619 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6562 (mt-10) REVERT: A 701 MET cc_start: 0.7076 (mmt) cc_final: 0.6868 (mmt) REVERT: A 732 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7145 (ttp80) REVERT: A 736 LYS cc_start: 0.7924 (tppt) cc_final: 0.7500 (ttmm) REVERT: A 765 GLU cc_start: 0.6765 (mp0) cc_final: 0.6407 (mp0) REVERT: A 848 LYS cc_start: 0.7263 (mmtm) cc_final: 0.7031 (mmtm) REVERT: A 870 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7409 (pp30) REVERT: A 956 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7137 (ttp) REVERT: A 959 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7557 (tp30) REVERT: A 1091 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6538 (t) REVERT: A 1104 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6769 (mm-30) REVERT: A 1105 PHE cc_start: 0.8132 (t80) cc_final: 0.7663 (t80) REVERT: A 1175 PHE cc_start: 0.8305 (m-80) cc_final: 0.8084 (m-80) REVERT: A 1222 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.6715 (m-30) REVERT: A 1223 ASP cc_start: 0.6772 (t0) cc_final: 0.6373 (t0) outliers start: 25 outliers final: 7 residues processed: 312 average time/residue: 0.2760 time to fit residues: 117.9848 Evaluate side-chains 301 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 288 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 956 MET Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 108 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 105 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 GLN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12055 Z= 0.221 Angle : 0.602 9.122 16184 Z= 0.318 Chirality : 0.041 0.175 1726 Planarity : 0.004 0.050 2127 Dihedral : 8.185 156.834 1604 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 2.02 % Allowed : 12.48 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.21), residues: 1441 helix: 0.96 (0.17), residues: 848 sheet: -1.78 (0.48), residues: 114 loop : -1.00 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1253 HIS 0.005 0.001 HIS A 833 PHE 0.025 0.002 PHE I 90 TYR 0.011 0.001 TYR A 812 ARG 0.008 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6532 (mmt) cc_final: 0.6146 (mmt) REVERT: B 77 MET cc_start: 0.6673 (pmm) cc_final: 0.6308 (pmm) REVERT: B 83 GLU cc_start: 0.6972 (tp30) cc_final: 0.6586 (tp30) REVERT: B 128 GLU cc_start: 0.6736 (tm-30) cc_final: 0.6445 (tm-30) REVERT: I 12 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7591 (tm-30) REVERT: I 38 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6836 (ttm110) REVERT: I 50 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7240 (tm-30) REVERT: I 73 MET cc_start: 0.7152 (tpt) cc_final: 0.5861 (tpt) REVERT: I 77 MET cc_start: 0.7540 (ptp) cc_final: 0.6525 (ptp) REVERT: I 92 VAL cc_start: 0.8406 (t) cc_final: 0.8190 (t) REVERT: I 107 ARG cc_start: 0.7377 (ttt-90) cc_final: 0.7053 (ttt-90) REVERT: I 146 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6161 (mmm) REVERT: A 16 PHE cc_start: 0.8085 (m-80) cc_final: 0.7505 (m-80) REVERT: A 24 ILE cc_start: 0.7840 (mt) cc_final: 0.7566 (mt) REVERT: A 56 LYS cc_start: 0.8200 (mppt) cc_final: 0.7800 (mppt) REVERT: A 61 ASP cc_start: 0.7172 (t70) cc_final: 0.6772 (t0) REVERT: A 138 MET cc_start: 0.7275 (tmm) cc_final: 0.7062 (ttp) REVERT: A 264 HIS cc_start: 0.7655 (m170) cc_final: 0.7391 (m170) REVERT: A 316 ASP cc_start: 0.6646 (m-30) cc_final: 0.4948 (m-30) REVERT: A 377 GLU cc_start: 0.7746 (tt0) cc_final: 0.7522 (tt0) REVERT: A 415 GLN cc_start: 0.7906 (mt0) cc_final: 0.7197 (mp10) REVERT: A 448 SER cc_start: 0.8230 (p) cc_final: 0.7995 (m) REVERT: A 491 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 580 ARG cc_start: 0.6900 (mpp80) cc_final: 0.6261 (mtt180) REVERT: A 603 MET cc_start: 0.7298 (tpt) cc_final: 0.6810 (tpt) REVERT: A 732 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7786 (ttp80) REVERT: A 733 LEU cc_start: 0.8353 (mt) cc_final: 0.8008 (mt) REVERT: A 765 GLU cc_start: 0.6783 (mp0) cc_final: 0.6412 (mp0) REVERT: A 807 LYS cc_start: 0.7651 (tttt) cc_final: 0.7441 (ttpt) REVERT: A 848 LYS cc_start: 0.7342 (mmtm) cc_final: 0.7110 (mmtm) REVERT: A 959 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: A 960 MET cc_start: 0.7756 (mmm) cc_final: 0.7227 (mmm) REVERT: A 1096 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: A 1105 PHE cc_start: 0.8082 (t80) cc_final: 0.7793 (t80) REVERT: A 1175 PHE cc_start: 0.8302 (m-80) cc_final: 0.8089 (m-80) REVERT: A 1202 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7916 (tt) outliers start: 26 outliers final: 12 residues processed: 303 average time/residue: 0.2935 time to fit residues: 120.4140 Evaluate side-chains 300 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 284 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1202 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN I 108 HIS ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN A 873 ASN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12055 Z= 0.277 Angle : 0.625 11.224 16184 Z= 0.327 Chirality : 0.043 0.198 1726 Planarity : 0.004 0.050 2127 Dihedral : 8.080 162.789 1598 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 2.56 % Allowed : 14.26 % Favored : 83.18 % 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: 0.08 (0.21), residues: 1441 helix: 0.99 (0.17), residues: 847 sheet: -1.87 (0.47), residues: 115 loop : -1.03 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1253 HIS 0.009 0.001 HIS I 108 PHE 0.040 0.002 PHE A 853 TYR 0.014 0.002 TYR A 812 ARG 0.010 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 287 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6595 (mmt) cc_final: 0.6186 (mmt) REVERT: B 77 MET cc_start: 0.6668 (pmm) cc_final: 0.6260 (pmm) REVERT: B 83 GLU cc_start: 0.7052 (tp30) cc_final: 0.6654 (tp30) REVERT: B 146 MET cc_start: 0.6705 (mmm) cc_final: 0.6349 (mmt) REVERT: I 50 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7336 (tm-30) REVERT: I 70 LEU cc_start: 0.8362 (tt) cc_final: 0.8097 (tt) REVERT: I 73 MET cc_start: 0.7090 (tpt) cc_final: 0.5974 (tpt) REVERT: I 77 MET cc_start: 0.7548 (ptp) cc_final: 0.6658 (ptp) REVERT: I 92 VAL cc_start: 0.8419 (t) cc_final: 0.8197 (t) REVERT: I 107 ARG cc_start: 0.7389 (ttt-90) cc_final: 0.7034 (ttt-90) REVERT: I 120 GLU cc_start: 0.7666 (pm20) cc_final: 0.7314 (pm20) REVERT: I 146 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6330 (mmm) REVERT: A 24 ILE cc_start: 0.7847 (mt) cc_final: 0.7574 (mt) REVERT: A 56 LYS cc_start: 0.8232 (mppt) cc_final: 0.7799 (mppt) REVERT: A 61 ASP cc_start: 0.7181 (t70) cc_final: 0.6748 (t0) REVERT: A 264 HIS cc_start: 0.7681 (m170) cc_final: 0.7427 (m170) REVERT: A 319 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.7010 (mtt-85) REVERT: A 377 GLU cc_start: 0.7744 (tt0) cc_final: 0.7542 (tt0) REVERT: A 448 SER cc_start: 0.8199 (p) cc_final: 0.7963 (m) REVERT: A 603 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6834 (tpt) REVERT: A 732 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7174 (ttp80) REVERT: A 736 LYS cc_start: 0.7926 (tppt) cc_final: 0.7461 (ttmm) REVERT: A 765 GLU cc_start: 0.6777 (mp0) cc_final: 0.6415 (mp0) REVERT: A 848 LYS cc_start: 0.7367 (mmtm) cc_final: 0.7123 (mmtm) REVERT: A 870 GLN cc_start: 0.7822 (pp30) cc_final: 0.7592 (tm-30) REVERT: A 956 MET cc_start: 0.7744 (tpp) cc_final: 0.7058 (tpp) REVERT: A 959 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: A 1096 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: A 1105 PHE cc_start: 0.8044 (t80) cc_final: 0.7832 (t80) REVERT: A 1207 GLU cc_start: 0.7371 (pm20) cc_final: 0.7125 (mp0) outliers start: 33 outliers final: 18 residues processed: 296 average time/residue: 0.3079 time to fit residues: 126.4582 Evaluate side-chains 306 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 284 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1132 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 42 GLN ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 821 GLN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12055 Z= 0.313 Angle : 0.637 8.950 16184 Z= 0.334 Chirality : 0.043 0.182 1726 Planarity : 0.004 0.053 2127 Dihedral : 8.185 172.892 1598 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 3.02 % Allowed : 15.74 % Favored : 81.24 % 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: 0.03 (0.21), residues: 1441 helix: 0.93 (0.17), residues: 848 sheet: -1.86 (0.48), residues: 115 loop : -1.04 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1253 HIS 0.007 0.001 HIS A 833 PHE 0.043 0.003 PHE A 853 TYR 0.015 0.002 TYR A 812 ARG 0.011 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 289 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6603 (mmt) cc_final: 0.6229 (mmt) REVERT: B 77 MET cc_start: 0.6663 (pmm) cc_final: 0.6288 (pmm) REVERT: B 83 GLU cc_start: 0.6999 (tp30) cc_final: 0.6599 (tp30) REVERT: I 12 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7511 (tm-30) REVERT: I 50 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7344 (tm-30) REVERT: I 70 LEU cc_start: 0.8382 (tt) cc_final: 0.8110 (tt) REVERT: I 72 MET cc_start: 0.6706 (mmt) cc_final: 0.6166 (mmt) REVERT: I 73 MET cc_start: 0.7073 (tpt) cc_final: 0.6066 (tpt) REVERT: I 77 MET cc_start: 0.7579 (ptp) cc_final: 0.6730 (ptp) REVERT: I 92 VAL cc_start: 0.8404 (t) cc_final: 0.8167 (t) REVERT: I 107 ARG cc_start: 0.7359 (ttt-90) cc_final: 0.7084 (ttt-90) REVERT: I 120 GLU cc_start: 0.7640 (pm20) cc_final: 0.7411 (pm20) REVERT: I 146 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6691 (mtm) REVERT: A 24 ILE cc_start: 0.7858 (mt) cc_final: 0.7585 (mt) REVERT: A 56 LYS cc_start: 0.8231 (mppt) cc_final: 0.7790 (mppt) REVERT: A 57 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7171 (mtmm) REVERT: A 61 ASP cc_start: 0.7138 (t70) cc_final: 0.6725 (t0) REVERT: A 197 THR cc_start: 0.7975 (m) cc_final: 0.7612 (p) REVERT: A 231 GLU cc_start: 0.6769 (tt0) cc_final: 0.6351 (tt0) REVERT: A 238 GLN cc_start: 0.6758 (tp-100) cc_final: 0.6412 (tp40) REVERT: A 264 HIS cc_start: 0.7668 (m170) cc_final: 0.7412 (m170) REVERT: A 319 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.6995 (mtt-85) REVERT: A 377 GLU cc_start: 0.7781 (tt0) cc_final: 0.7557 (tt0) REVERT: A 415 GLN cc_start: 0.7921 (mt0) cc_final: 0.7138 (pm20) REVERT: A 448 SER cc_start: 0.8198 (p) cc_final: 0.7970 (m) REVERT: A 702 GLN cc_start: 0.7733 (tt0) cc_final: 0.7531 (tt0) REVERT: A 732 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7160 (ttp80) REVERT: A 736 LYS cc_start: 0.7973 (tppt) cc_final: 0.7465 (ttmm) REVERT: A 765 GLU cc_start: 0.6787 (mp0) cc_final: 0.6448 (mp0) REVERT: A 848 LYS cc_start: 0.7389 (mmtm) cc_final: 0.7150 (mmtm) REVERT: A 956 MET cc_start: 0.7747 (tpp) cc_final: 0.7404 (tpp) REVERT: A 959 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: A 1084 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7217 (tp30) REVERT: A 1089 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7647 (tt) REVERT: A 1096 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6659 (pm20) REVERT: A 1171 PHE cc_start: 0.7964 (m-80) cc_final: 0.7747 (m-80) outliers start: 39 outliers final: 24 residues processed: 305 average time/residue: 0.2915 time to fit residues: 120.5055 Evaluate side-chains 316 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 287 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.1980 chunk 125 optimal weight: 30.0000 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 134 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 42 GLN A 597 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12055 Z= 0.232 Angle : 0.625 8.935 16184 Z= 0.323 Chirality : 0.042 0.177 1726 Planarity : 0.004 0.053 2127 Dihedral : 8.003 175.442 1598 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 2.56 % Allowed : 16.51 % Favored : 80.93 % 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: 0.28 (0.22), residues: 1441 helix: 1.12 (0.17), residues: 848 sheet: -1.74 (0.48), residues: 112 loop : -0.93 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1253 HIS 0.005 0.001 HIS A 833 PHE 0.041 0.002 PHE A 853 TYR 0.013 0.001 TYR A1082 ARG 0.011 0.001 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 288 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6617 (pmm) cc_final: 0.6239 (pmm) REVERT: B 83 GLU cc_start: 0.6954 (tp30) cc_final: 0.6536 (tp30) REVERT: I 12 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7571 (tm-30) REVERT: I 40 LEU cc_start: 0.6435 (mm) cc_final: 0.6160 (mm) REVERT: I 50 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7364 (tm-30) REVERT: I 70 LEU cc_start: 0.8365 (tt) cc_final: 0.8099 (tt) REVERT: I 73 MET cc_start: 0.7122 (tpt) cc_final: 0.6142 (tpt) REVERT: I 77 MET cc_start: 0.7617 (ptp) cc_final: 0.6842 (ptp) REVERT: I 92 VAL cc_start: 0.8406 (t) cc_final: 0.8164 (t) REVERT: I 107 ARG cc_start: 0.7360 (ttt-90) cc_final: 0.7067 (ttt-90) REVERT: I 110 MET cc_start: 0.7187 (mpp) cc_final: 0.6966 (mpp) REVERT: I 120 GLU cc_start: 0.7654 (pm20) cc_final: 0.7365 (pm20) REVERT: I 146 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6543 (mtm) REVERT: A 24 ILE cc_start: 0.7839 (mt) cc_final: 0.7601 (mt) REVERT: A 56 LYS cc_start: 0.8228 (mppt) cc_final: 0.7778 (mppt) REVERT: A 61 ASP cc_start: 0.7112 (t70) cc_final: 0.6681 (t0) REVERT: A 231 GLU cc_start: 0.6809 (tt0) cc_final: 0.6580 (tt0) REVERT: A 264 HIS cc_start: 0.7634 (m170) cc_final: 0.7389 (m170) REVERT: A 319 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.6998 (mtt-85) REVERT: A 377 GLU cc_start: 0.7742 (tt0) cc_final: 0.7475 (tt0) REVERT: A 415 GLN cc_start: 0.7930 (mt0) cc_final: 0.7194 (mp10) REVERT: A 448 SER cc_start: 0.8234 (p) cc_final: 0.8009 (m) REVERT: A 596 LYS cc_start: 0.8145 (mptt) cc_final: 0.7610 (mmtp) REVERT: A 603 MET cc_start: 0.7359 (tpt) cc_final: 0.7041 (tpt) REVERT: A 732 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7797 (ttp80) REVERT: A 765 GLU cc_start: 0.6770 (mp0) cc_final: 0.6407 (mp0) REVERT: A 848 LYS cc_start: 0.7357 (mmtm) cc_final: 0.7103 (mmtm) REVERT: A 956 MET cc_start: 0.7674 (tpp) cc_final: 0.7360 (tpp) REVERT: A 959 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7198 (tt0) outliers start: 33 outliers final: 19 residues processed: 302 average time/residue: 0.2880 time to fit residues: 117.9482 Evaluate side-chains 299 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 278 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1202 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 GLN A1264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12055 Z= 0.269 Angle : 0.657 12.176 16184 Z= 0.339 Chirality : 0.043 0.174 1726 Planarity : 0.004 0.053 2127 Dihedral : 7.664 163.522 1595 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 2.71 % Allowed : 17.60 % Favored : 79.69 % 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: 0.22 (0.21), residues: 1441 helix: 1.05 (0.17), residues: 849 sheet: -1.81 (0.47), residues: 113 loop : -0.90 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1253 HIS 0.006 0.001 HIS A 833 PHE 0.036 0.002 PHE A 451 TYR 0.013 0.002 TYR A1082 ARG 0.013 0.001 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6640 (pmm) cc_final: 0.6255 (pmm) REVERT: B 83 GLU cc_start: 0.6982 (tp30) cc_final: 0.6559 (tp30) REVERT: I 6 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7234 (t) REVERT: I 50 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7392 (tm-30) REVERT: I 70 LEU cc_start: 0.8394 (tt) cc_final: 0.8137 (tt) REVERT: I 73 MET cc_start: 0.6917 (tpt) cc_final: 0.6003 (tpt) REVERT: I 77 MET cc_start: 0.7613 (ptp) cc_final: 0.6661 (ptp) REVERT: I 92 VAL cc_start: 0.8403 (t) cc_final: 0.8167 (t) REVERT: I 101 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6388 (mm) REVERT: I 107 ARG cc_start: 0.7355 (ttt-90) cc_final: 0.6969 (ttt-90) REVERT: I 110 MET cc_start: 0.7265 (mpp) cc_final: 0.6902 (mpp) REVERT: I 146 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6509 (mtm) REVERT: A 23 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.6834 (t70) REVERT: A 24 ILE cc_start: 0.7828 (mt) cc_final: 0.7398 (mt) REVERT: A 56 LYS cc_start: 0.8260 (mppt) cc_final: 0.7815 (mppt) REVERT: A 61 ASP cc_start: 0.7119 (t70) cc_final: 0.6708 (t0) REVERT: A 196 LYS cc_start: 0.8163 (tttm) cc_final: 0.7949 (tttp) REVERT: A 197 THR cc_start: 0.7623 (m) cc_final: 0.7396 (t) REVERT: A 231 GLU cc_start: 0.6861 (tt0) cc_final: 0.6582 (tt0) REVERT: A 264 HIS cc_start: 0.7632 (m170) cc_final: 0.7375 (m170) REVERT: A 319 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7047 (mtt-85) REVERT: A 377 GLU cc_start: 0.7749 (tt0) cc_final: 0.7481 (tt0) REVERT: A 448 SER cc_start: 0.8217 (p) cc_final: 0.8012 (m) REVERT: A 596 LYS cc_start: 0.8147 (mptt) cc_final: 0.7900 (mttm) REVERT: A 603 MET cc_start: 0.7367 (tpt) cc_final: 0.6933 (tpt) REVERT: A 701 MET cc_start: 0.7075 (mmt) cc_final: 0.6788 (mmt) REVERT: A 732 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7775 (ttp80) REVERT: A 765 GLU cc_start: 0.6766 (mp0) cc_final: 0.6388 (mp0) REVERT: A 848 LYS cc_start: 0.7353 (mmtm) cc_final: 0.7127 (mmtm) REVERT: A 956 MET cc_start: 0.7660 (tpp) cc_final: 0.7363 (tpp) REVERT: A 959 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: A 1084 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7211 (tp30) outliers start: 35 outliers final: 21 residues processed: 305 average time/residue: 0.2940 time to fit residues: 123.0314 Evaluate side-chains 310 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 283 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1202 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 109 optimal weight: 0.0980 chunk 126 optimal weight: 10.0000 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 GLN A1264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12055 Z= 0.218 Angle : 0.638 8.790 16184 Z= 0.328 Chirality : 0.042 0.169 1726 Planarity : 0.004 0.052 2127 Dihedral : 7.444 156.523 1595 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 2.56 % Allowed : 18.45 % Favored : 78.99 % 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: 0.40 (0.22), residues: 1441 helix: 1.19 (0.17), residues: 849 sheet: -1.73 (0.48), residues: 113 loop : -0.80 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1253 HIS 0.004 0.001 HIS A 833 PHE 0.029 0.002 PHE A 451 TYR 0.012 0.001 TYR A1082 ARG 0.008 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 283 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6629 (pmm) cc_final: 0.6240 (pmm) REVERT: B 83 GLU cc_start: 0.6937 (tp30) cc_final: 0.6506 (tp30) REVERT: I 50 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7361 (tm-30) REVERT: I 70 LEU cc_start: 0.8413 (tt) cc_final: 0.8173 (tt) REVERT: I 73 MET cc_start: 0.6900 (tpt) cc_final: 0.5938 (tpt) REVERT: I 77 MET cc_start: 0.7587 (ptp) cc_final: 0.6542 (ptp) REVERT: I 92 VAL cc_start: 0.8412 (t) cc_final: 0.8187 (t) REVERT: I 107 ARG cc_start: 0.7346 (ttt-90) cc_final: 0.6966 (ttt-90) REVERT: I 110 MET cc_start: 0.7264 (mpp) cc_final: 0.6895 (mpp) REVERT: I 146 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6455 (mtm) REVERT: A 24 ILE cc_start: 0.7838 (mt) cc_final: 0.7617 (mt) REVERT: A 57 LYS cc_start: 0.7368 (mtmt) cc_final: 0.7042 (mtmt) REVERT: A 61 ASP cc_start: 0.7128 (t70) cc_final: 0.6713 (t0) REVERT: A 196 LYS cc_start: 0.8075 (tttm) cc_final: 0.7701 (ttmt) REVERT: A 197 THR cc_start: 0.7577 (m) cc_final: 0.7330 (t) REVERT: A 231 GLU cc_start: 0.6868 (tt0) cc_final: 0.6498 (tt0) REVERT: A 264 HIS cc_start: 0.7586 (m170) cc_final: 0.7310 (m170) REVERT: A 319 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.7023 (mtt-85) REVERT: A 377 GLU cc_start: 0.7749 (tt0) cc_final: 0.7471 (tt0) REVERT: A 448 SER cc_start: 0.8174 (p) cc_final: 0.7969 (m) REVERT: A 603 MET cc_start: 0.7374 (tpt) cc_final: 0.6814 (tpt) REVERT: A 701 MET cc_start: 0.7067 (mmt) cc_final: 0.6788 (mmt) REVERT: A 732 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7801 (ttp80) REVERT: A 765 GLU cc_start: 0.6771 (mp0) cc_final: 0.6402 (mp0) REVERT: A 848 LYS cc_start: 0.7355 (mmtm) cc_final: 0.7120 (mmtm) REVERT: A 956 MET cc_start: 0.7643 (tpp) cc_final: 0.7353 (tpp) REVERT: A 959 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: A 1084 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7192 (tp30) outliers start: 33 outliers final: 19 residues processed: 299 average time/residue: 0.3116 time to fit residues: 127.7276 Evaluate side-chains 304 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 282 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1132 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 GLN A 176 GLN A 597 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 GLN A1264 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12055 Z= 0.262 Angle : 0.679 12.284 16184 Z= 0.348 Chirality : 0.043 0.301 1726 Planarity : 0.004 0.052 2127 Dihedral : 7.300 143.749 1595 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.75 % Favored : 96.18 % Rotamer: Outliers : 2.33 % Allowed : 19.07 % Favored : 78.60 % 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: 0.31 (0.22), residues: 1441 helix: 1.09 (0.17), residues: 853 sheet: -1.76 (0.48), residues: 113 loop : -0.78 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1253 HIS 0.006 0.001 HIS A 833 PHE 0.029 0.002 PHE A 445 TYR 0.015 0.002 TYR A 100 ARG 0.009 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 288 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6635 (pmm) cc_final: 0.6271 (pmm) REVERT: B 83 GLU cc_start: 0.6983 (tp30) cc_final: 0.6527 (tp30) REVERT: I 70 LEU cc_start: 0.8361 (tt) cc_final: 0.8076 (tt) REVERT: I 73 MET cc_start: 0.6938 (tpt) cc_final: 0.5911 (tpt) REVERT: I 77 MET cc_start: 0.7563 (ptp) cc_final: 0.6558 (ptp) REVERT: I 92 VAL cc_start: 0.8384 (t) cc_final: 0.8160 (t) REVERT: I 101 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6340 (mm) REVERT: I 107 ARG cc_start: 0.7358 (ttt-90) cc_final: 0.6948 (ttt-90) REVERT: I 110 MET cc_start: 0.7284 (mpp) cc_final: 0.6857 (mpp) REVERT: I 146 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.6475 (mtm) REVERT: A 23 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.6812 (t70) REVERT: A 24 ILE cc_start: 0.7814 (mt) cc_final: 0.7389 (mt) REVERT: A 57 LYS cc_start: 0.7400 (mtmt) cc_final: 0.7120 (mtmm) REVERT: A 61 ASP cc_start: 0.7128 (t70) cc_final: 0.6736 (t0) REVERT: A 88 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 197 THR cc_start: 0.7595 (m) cc_final: 0.7356 (t) REVERT: A 231 GLU cc_start: 0.6881 (tt0) cc_final: 0.6290 (tt0) REVERT: A 234 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7150 (mtt90) REVERT: A 264 HIS cc_start: 0.7614 (m170) cc_final: 0.7305 (m170) REVERT: A 319 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7023 (mtt-85) REVERT: A 383 GLN cc_start: 0.8022 (mm110) cc_final: 0.7795 (mm110) REVERT: A 387 ARG cc_start: 0.7528 (ptt180) cc_final: 0.7178 (ptt180) REVERT: A 415 GLN cc_start: 0.7954 (mt0) cc_final: 0.7248 (mp10) REVERT: A 448 SER cc_start: 0.8180 (p) cc_final: 0.7977 (m) REVERT: A 596 LYS cc_start: 0.8131 (mptt) cc_final: 0.7882 (mttm) REVERT: A 603 MET cc_start: 0.7399 (tpt) cc_final: 0.6781 (tpt) REVERT: A 701 MET cc_start: 0.7092 (mmt) cc_final: 0.6846 (mmt) REVERT: A 732 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7794 (ttp80) REVERT: A 765 GLU cc_start: 0.6776 (mp0) cc_final: 0.6378 (mp0) REVERT: A 956 MET cc_start: 0.7664 (tpp) cc_final: 0.7365 (tpp) REVERT: A 959 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: A 1084 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: A 1104 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6995 (mm-30) outliers start: 30 outliers final: 19 residues processed: 306 average time/residue: 0.2859 time to fit residues: 119.5671 Evaluate side-chains 309 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 283 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1252 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 GLN A1264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12055 Z= 0.266 Angle : 0.680 8.553 16184 Z= 0.352 Chirality : 0.044 0.238 1726 Planarity : 0.004 0.052 2127 Dihedral : 7.241 136.350 1595 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 2.40 % Allowed : 19.69 % Favored : 77.91 % 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: 0.30 (0.22), residues: 1441 helix: 1.05 (0.17), residues: 852 sheet: -1.76 (0.48), residues: 111 loop : -0.73 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1253 HIS 0.006 0.001 HIS A 833 PHE 0.028 0.002 PHE A1105 TYR 0.014 0.002 TYR A 100 ARG 0.009 0.000 ARG I 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 287 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6615 (pmm) cc_final: 0.6225 (pmm) REVERT: B 83 GLU cc_start: 0.6978 (tp30) cc_final: 0.6542 (tp30) REVERT: I 50 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7473 (tm-30) REVERT: I 70 LEU cc_start: 0.8439 (tt) cc_final: 0.8148 (tt) REVERT: I 73 MET cc_start: 0.6935 (tpt) cc_final: 0.5977 (tpt) REVERT: I 77 MET cc_start: 0.7591 (ptp) cc_final: 0.6580 (ptp) REVERT: I 92 VAL cc_start: 0.8399 (t) cc_final: 0.8160 (t) REVERT: I 101 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6338 (mm) REVERT: I 107 ARG cc_start: 0.7361 (ttt-90) cc_final: 0.6935 (ttt-90) REVERT: I 110 MET cc_start: 0.7287 (mpp) cc_final: 0.6844 (mpp) REVERT: I 146 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6452 (mtm) REVERT: A 23 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.6825 (t70) REVERT: A 24 ILE cc_start: 0.7806 (mt) cc_final: 0.7388 (mt) REVERT: A 57 LYS cc_start: 0.7390 (mtmt) cc_final: 0.7082 (mtmm) REVERT: A 61 ASP cc_start: 0.7118 (t70) cc_final: 0.6744 (t0) REVERT: A 88 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7796 (t) REVERT: A 197 THR cc_start: 0.7612 (m) cc_final: 0.7336 (t) REVERT: A 231 GLU cc_start: 0.6856 (tt0) cc_final: 0.6356 (tt0) REVERT: A 234 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7267 (mtt90) REVERT: A 237 VAL cc_start: 0.8235 (t) cc_final: 0.7870 (p) REVERT: A 264 HIS cc_start: 0.7606 (m170) cc_final: 0.7290 (m170) REVERT: A 319 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7013 (mtt-85) REVERT: A 383 GLN cc_start: 0.8005 (mm110) cc_final: 0.7774 (mm110) REVERT: A 387 ARG cc_start: 0.7480 (ptt180) cc_final: 0.7225 (ptt180) REVERT: A 415 GLN cc_start: 0.7960 (mt0) cc_final: 0.7207 (pm20) REVERT: A 603 MET cc_start: 0.7408 (tpt) cc_final: 0.6704 (tpt) REVERT: A 701 MET cc_start: 0.7093 (mmt) cc_final: 0.6838 (mmt) REVERT: A 732 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7782 (ttp80) REVERT: A 765 GLU cc_start: 0.6778 (mp0) cc_final: 0.6392 (mp0) REVERT: A 848 LYS cc_start: 0.7345 (mmtm) cc_final: 0.7117 (mmtm) REVERT: A 872 LYS cc_start: 0.8500 (mttp) cc_final: 0.8027 (mptp) REVERT: A 956 MET cc_start: 0.7686 (tpp) cc_final: 0.7457 (tpp) REVERT: A 959 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: A 1084 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: A 1104 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6999 (mm-30) outliers start: 31 outliers final: 23 residues processed: 303 average time/residue: 0.2895 time to fit residues: 121.0450 Evaluate side-chains 306 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 276 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1252 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 114 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 0.0050 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 0.0670 overall best weight: 0.2910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 GLN A1264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.162320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138877 restraints weight = 19132.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143528 restraints weight = 9226.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.146566 restraints weight = 5531.038| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12055 Z= 0.192 Angle : 0.663 8.627 16184 Z= 0.339 Chirality : 0.042 0.192 1726 Planarity : 0.004 0.052 2127 Dihedral : 6.924 141.589 1595 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.09 % Rotamer: Outliers : 2.33 % Allowed : 19.77 % Favored : 77.91 % 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: 0.65 (0.22), residues: 1441 helix: 1.32 (0.17), residues: 855 sheet: -1.40 (0.50), residues: 110 loop : -0.64 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1253 HIS 0.004 0.001 HIS A 833 PHE 0.028 0.002 PHE A 445 TYR 0.012 0.001 TYR A1082 ARG 0.010 0.001 ARG I 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3107.32 seconds wall clock time: 56 minutes 10.02 seconds (3370.02 seconds total)