Starting phenix.real_space_refine on Wed Feb 12 13:36:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8izq_35868/02_2025/8izq_35868.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izq_35868/02_2025/8izq_35868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8izq_35868/02_2025/8izq_35868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izq_35868/02_2025/8izq_35868.map" model { file = "/net/cci-nas-00/data/ceres_data/8izq_35868/02_2025/8izq_35868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izq_35868/02_2025/8izq_35868.cif" } resolution = 3.31 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5173 2.51 5 N 1290 2.21 5 O 1419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7924 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7924 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 967} Chain breaks: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.01, per 1000 atoms: 0.63 Number of scatterers: 7924 At special positions: 0 Unit cell: (88.81, 103.79, 153.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1419 8.00 N 1290 7.00 C 5173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 3 sheets defined 74.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.626A pdb=" N CYS A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 33 through 54 removed outlier: 3.542A pdb=" N LEU A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.158A pdb=" N VAL A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 removed outlier: 4.195A pdb=" N GLY A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 121 removed outlier: 3.855A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.581A pdb=" N GLY A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 130 through 138 removed outlier: 4.633A pdb=" N TRP A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 4.389A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 184 removed outlier: 3.626A pdb=" N GLN A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 179 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 234 through 265 removed outlier: 3.751A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.818A pdb=" N LYS A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 356 through 405 removed outlier: 4.380A pdb=" N GLY A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.854A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.808A pdb=" N ASN A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 437' Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.610A pdb=" N ILE A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.855A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 569 Proline residue: A 554 - end of helix removed outlier: 4.284A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 588 removed outlier: 4.030A pdb=" N THR A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 613 removed outlier: 3.752A pdb=" N LEU A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Proline residue: A 597 - end of helix removed outlier: 3.656A pdb=" N SER A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 removed outlier: 5.025A pdb=" N LEU A 617 " --> pdb=" O GLU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.707A pdb=" N LEU A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.713A pdb=" N GLN A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 748 through 752 removed outlier: 4.033A pdb=" N LEU A 751 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 778 removed outlier: 3.506A pdb=" N LEU A 771 " --> pdb=" O GLN A 767 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 805 removed outlier: 3.522A pdb=" N ASN A 801 " --> pdb=" O LYS A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 828 removed outlier: 3.624A pdb=" N GLN A 827 " --> pdb=" O PHE A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 852 Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.627A pdb=" N LYS A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 975 removed outlier: 3.618A pdb=" N ALA A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1010 removed outlier: 4.152A pdb=" N MET A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A1007 " --> pdb=" O TRP A1003 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS A1008 " --> pdb=" O THR A1004 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1044 Processing helix chain 'A' and resid 1097 through 1120 removed outlier: 3.979A pdb=" N TRP A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A1103 " --> pdb=" O LEU A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1169 removed outlier: 3.882A pdb=" N ILE A1126 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A1128 " --> pdb=" O THR A1124 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 3.651A pdb=" N ILE A1133 " --> pdb=" O PRO A1129 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A1143 " --> pdb=" O MET A1139 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.650A pdb=" N PHE A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A1164 " --> pdb=" O TYR A1160 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1174 removed outlier: 3.527A pdb=" N ILE A1173 " --> pdb=" O GLY A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1229 removed outlier: 3.764A pdb=" N PHE A1182 " --> pdb=" O HIS A1178 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A1187 " --> pdb=" O LEU A1183 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A1188 " --> pdb=" O LYS A1184 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A1189 " --> pdb=" O HIS A1185 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A1209 " --> pdb=" O ARG A1205 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1245 Processing helix chain 'A' and resid 1247 through 1265 removed outlier: 3.598A pdb=" N TRP A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG A1257 " --> pdb=" O ASN A1253 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A1258 " --> pdb=" O TRP A1254 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A1262 " --> pdb=" O MET A1258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 630 removed outlier: 3.543A pdb=" N ARG A 628 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A 697 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 654 through 657 removed outlier: 3.568A pdb=" N VAL A 654 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA A 642 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR A 645 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASN A 690 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 781 through 785 removed outlier: 3.626A pdb=" N LEU A 816 " --> pdb=" O TYR A 782 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 818 " --> pdb=" O LEU A 784 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 667 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA A 668 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 834 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 670 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 841 " --> pdb=" O VAL A 833 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1308 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: 2.44 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1240 1.30 - 1.43: 2214 1.43 - 1.56: 4577 1.56 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 8101 Sorted by residual: bond pdb=" CA SER A1243 " pdb=" CB SER A1243 " ideal model delta sigma weight residual 1.537 1.453 0.084 1.41e-02 5.03e+03 3.54e+01 bond pdb=" CA SER A 325 " pdb=" CB SER A 325 " ideal model delta sigma weight residual 1.536 1.451 0.085 1.46e-02 4.69e+03 3.37e+01 bond pdb=" CA SER A 202 " pdb=" CB SER A 202 " ideal model delta sigma weight residual 1.536 1.454 0.082 1.42e-02 4.96e+03 3.33e+01 bond pdb=" CA SER A 609 " pdb=" CB SER A 609 " ideal model delta sigma weight residual 1.528 1.450 0.078 1.59e-02 3.96e+03 2.42e+01 bond pdb=" N ARG A 219 " pdb=" CA ARG A 219 " ideal model delta sigma weight residual 1.456 1.498 -0.043 8.70e-03 1.32e+04 2.40e+01 ... (remaining 8096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 8880 2.70 - 5.40: 1822 5.40 - 8.10: 247 8.10 - 10.80: 33 10.80 - 13.49: 13 Bond angle restraints: 10995 Sorted by residual: angle pdb=" N LEU A 431 " pdb=" CA LEU A 431 " pdb=" C LEU A 431 " ideal model delta sigma weight residual 113.17 101.73 11.44 1.26e+00 6.30e-01 8.24e+01 angle pdb=" N THR A1237 " pdb=" CA THR A1237 " pdb=" C THR A1237 " ideal model delta sigma weight residual 111.36 102.05 9.31 1.09e+00 8.42e-01 7.29e+01 angle pdb=" C PRO A 597 " pdb=" CA PRO A 597 " pdb=" CB PRO A 597 " ideal model delta sigma weight residual 113.06 99.57 13.49 1.59e+00 3.96e-01 7.20e+01 angle pdb=" N ILE A 140 " pdb=" CA ILE A 140 " pdb=" C ILE A 140 " ideal model delta sigma weight residual 112.17 104.31 7.86 9.50e-01 1.11e+00 6.84e+01 angle pdb=" N LEU A 343 " pdb=" CA LEU A 343 " pdb=" C LEU A 343 " ideal model delta sigma weight residual 113.16 103.11 10.05 1.24e+00 6.50e-01 6.57e+01 ... (remaining 10990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4043 17.35 - 34.69: 469 34.69 - 52.03: 195 52.03 - 69.38: 63 69.38 - 86.72: 8 Dihedral angle restraints: 4778 sinusoidal: 1867 harmonic: 2911 Sorted by residual: dihedral pdb=" C THR A 30 " pdb=" N THR A 30 " pdb=" CA THR A 30 " pdb=" CB THR A 30 " ideal model delta harmonic sigma weight residual -122.00 -143.70 21.70 0 2.50e+00 1.60e-01 7.53e+01 dihedral pdb=" C PHE A1240 " pdb=" N PHE A1240 " pdb=" CA PHE A1240 " pdb=" CB PHE A1240 " ideal model delta harmonic sigma weight residual -122.60 -139.40 16.80 0 2.50e+00 1.60e-01 4.52e+01 dihedral pdb=" C THR A1112 " pdb=" N THR A1112 " pdb=" CA THR A1112 " pdb=" CB THR A1112 " ideal model delta harmonic sigma weight residual -122.00 -105.26 -16.74 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 4775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 933 0.148 - 0.297: 305 0.297 - 0.445: 50 0.445 - 0.593: 4 0.593 - 0.741: 1 Chirality restraints: 1293 Sorted by residual: chirality pdb=" CA THR A 30 " pdb=" N THR A 30 " pdb=" C THR A 30 " pdb=" CB THR A 30 " both_signs ideal model delta sigma weight residual False 2.53 1.78 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA PHE A1240 " pdb=" N PHE A1240 " pdb=" C PHE A1240 " pdb=" CB PHE A1240 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CA GLU A1165 " pdb=" N GLU A1165 " pdb=" C GLU A1165 " pdb=" CB GLU A1165 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.57e+00 ... (remaining 1290 not shown) Planarity restraints: 1349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1146 " 0.487 9.50e-02 1.11e+02 2.18e-01 2.91e+01 pdb=" NE ARG A1146 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A1146 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A1146 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1146 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1205 " 0.485 9.50e-02 1.11e+02 2.17e-01 2.89e+01 pdb=" NE ARG A1205 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A1205 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A1205 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1205 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 318 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C PHE A 318 " 0.074 2.00e-02 2.50e+03 pdb=" O PHE A 318 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR A 319 " -0.026 2.00e-02 2.50e+03 ... (remaining 1346 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 34 2.49 - 3.09: 6369 3.09 - 3.69: 11721 3.69 - 4.30: 17072 4.30 - 4.90: 26815 Nonbonded interactions: 62011 Sorted by model distance: nonbonded pdb=" O LYS A 802 " pdb=" N LEU A 809 " model vdw 1.886 3.120 nonbonded pdb=" N TRP A 309 " pdb=" OE2 GLU A 614 " model vdw 2.162 3.120 nonbonded pdb=" O SER A1161 " pdb=" N SER A1164 " model vdw 2.198 3.120 nonbonded pdb=" C THR A 61 " pdb=" OG1 THR A 61 " model vdw 2.319 2.616 nonbonded pdb=" O THR A 205 " pdb=" CG2 THR A 205 " model vdw 2.356 3.460 ... (remaining 62006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.550 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.014 0.085 8101 Z= 0.900 Angle : 2.195 13.495 10995 Z= 1.638 Chirality : 0.144 0.741 1293 Planarity : 0.013 0.218 1349 Dihedral : 18.769 86.721 2883 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.27 % Favored : 95.43 % Rotamer: Outliers : 17.51 % Allowed : 17.85 % Favored : 64.63 % Cbeta Deviations : 4.55 % 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: -1.26 (0.25), residues: 984 helix: -0.53 (0.19), residues: 665 sheet: 0.04 (0.95), residues: 37 loop : -1.36 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 358 HIS 0.011 0.002 HIS A 692 PHE 0.033 0.003 PHE A 174 TYR 0.031 0.004 TYR A1015 ARG 0.004 0.001 ARG A1230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 215 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.5910 (ttt180) REVERT: A 107 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: A 124 CYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7447 (m) REVERT: A 148 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6207 (tp40) REVERT: A 311 MET cc_start: 0.7170 (mtm) cc_final: 0.6951 (mtt) REVERT: A 324 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7731 (mttm) REVERT: A 419 GLU cc_start: 0.7591 (tm-30) cc_final: 0.6842 (tm-30) REVERT: A 424 MET cc_start: 0.9338 (mtt) cc_final: 0.8715 (mtt) REVERT: A 440 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.6670 (mpt) REVERT: A 446 LEU cc_start: 0.9065 (tp) cc_final: 0.8841 (tp) REVERT: A 596 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 692 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.6767 (p-80) REVERT: A 712 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7805 (m110) REVERT: A 724 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: A 734 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8586 (mm) REVERT: A 1019 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7110 (tm-30) REVERT: A 1022 MET cc_start: 0.8523 (tpp) cc_final: 0.8308 (tpt) REVERT: A 1042 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.7144 (m-70) REVERT: A 1141 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7649 (t80) REVERT: A 1186 ASN cc_start: 0.7540 (OUTLIER) cc_final: 0.6955 (t0) REVERT: A 1198 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5980 (t80) outliers start: 155 outliers final: 51 residues processed: 330 average time/residue: 0.2004 time to fit residues: 88.8739 Evaluate side-chains 212 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 147 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 306 PRO Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 631 CYS Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1141 TYR Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1198 PHE Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1258 MET Chi-restraints excluded: chain A residue 1264 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN A 128 ASN A 187 ASN A 245 HIS A 332 ASN A 447 GLN A 551 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN A 692 HIS A 711 GLN A 732 GLN ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS A1185 HIS ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1253 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.164973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.122842 restraints weight = 12235.874| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.51 r_work: 0.3544 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8101 Z= 0.251 Angle : 0.753 10.081 10995 Z= 0.400 Chirality : 0.044 0.236 1293 Planarity : 0.005 0.062 1349 Dihedral : 11.458 73.661 1176 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 9.27 % Allowed : 22.49 % Favored : 68.25 % 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: -0.39 (0.26), residues: 984 helix: 0.34 (0.20), residues: 662 sheet: -1.23 (0.98), residues: 27 loop : -1.36 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 456 HIS 0.011 0.001 HIS A 823 PHE 0.043 0.002 PHE A 174 TYR 0.021 0.002 TYR A 730 ARG 0.007 0.001 ARG A1205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 173 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5455 (OUTLIER) cc_final: 0.4698 (ttt180) REVERT: A 124 CYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8264 (m) REVERT: A 148 GLN cc_start: 0.5799 (OUTLIER) cc_final: 0.5066 (tp40) REVERT: A 177 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5787 (tt) REVERT: A 227 TRP cc_start: 0.6910 (m-10) cc_final: 0.6670 (m-10) REVERT: A 238 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7869 (mt) REVERT: A 247 LYS cc_start: 0.7925 (mttt) cc_final: 0.7667 (mtmm) REVERT: A 311 MET cc_start: 0.6249 (mtm) cc_final: 0.6040 (mtt) REVERT: A 324 LYS cc_start: 0.7294 (mtmt) cc_final: 0.7030 (mttp) REVERT: A 385 CYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6977 (m) REVERT: A 424 MET cc_start: 0.9271 (mtt) cc_final: 0.8867 (mtt) REVERT: A 596 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6774 (mp) REVERT: A 620 ASP cc_start: 0.7300 (t0) cc_final: 0.6947 (p0) REVERT: A 646 TRP cc_start: 0.8054 (t-100) cc_final: 0.7728 (t-100) REVERT: A 760 ASN cc_start: 0.6469 (OUTLIER) cc_final: 0.6039 (p0) REVERT: A 765 GLN cc_start: 0.8026 (mp10) cc_final: 0.7601 (mp10) REVERT: A 768 ARG cc_start: 0.8465 (mtt180) cc_final: 0.7771 (mtt90) REVERT: A 828 VAL cc_start: 0.8492 (t) cc_final: 0.8211 (p) REVERT: A 1019 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6161 (tm-30) REVERT: A 1022 MET cc_start: 0.6930 (tpp) cc_final: 0.6651 (tpp) outliers start: 82 outliers final: 45 residues processed: 234 average time/residue: 0.1857 time to fit residues: 60.1726 Evaluate side-chains 191 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 631 CYS Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1264 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN A1042 HIS A1244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.163586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.121207 restraints weight = 12131.947| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.40 r_work: 0.3512 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8101 Z= 0.231 Angle : 0.651 8.702 10995 Z= 0.340 Chirality : 0.041 0.167 1293 Planarity : 0.004 0.056 1349 Dihedral : 9.494 68.530 1121 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.10 % Allowed : 26.89 % Favored : 67.01 % 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: 0.07 (0.26), residues: 984 helix: 0.68 (0.20), residues: 672 sheet: -0.48 (1.20), residues: 20 loop : -1.28 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 456 HIS 0.004 0.001 HIS A 820 PHE 0.033 0.002 PHE A 174 TYR 0.019 0.002 TYR A 730 ARG 0.006 0.001 ARG A1205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 155 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5499 (tpt170) cc_final: 0.4737 (ttt-90) REVERT: A 138 LEU cc_start: 0.8423 (mp) cc_final: 0.7648 (tt) REVERT: A 148 GLN cc_start: 0.5829 (OUTLIER) cc_final: 0.5019 (tp40) REVERT: A 177 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5737 (tt) REVERT: A 227 TRP cc_start: 0.7063 (m-10) cc_final: 0.6808 (m-10) REVERT: A 311 MET cc_start: 0.6290 (mtm) cc_final: 0.5730 (mmt) REVERT: A 320 MET cc_start: 0.6623 (mmt) cc_final: 0.6204 (tpp) REVERT: A 324 LYS cc_start: 0.7425 (mtmt) cc_final: 0.7096 (mttp) REVERT: A 424 MET cc_start: 0.9240 (mtt) cc_final: 0.8969 (mtt) REVERT: A 620 ASP cc_start: 0.7386 (t0) cc_final: 0.6914 (p0) REVERT: A 621 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7633 (p0) REVERT: A 637 MET cc_start: 0.5709 (ptp) cc_final: 0.5371 (ptp) REVERT: A 646 TRP cc_start: 0.8054 (t-100) cc_final: 0.7619 (t-100) REVERT: A 712 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7780 (m110) REVERT: A 734 LEU cc_start: 0.8494 (mm) cc_final: 0.8256 (mm) REVERT: A 739 LEU cc_start: 0.8468 (tt) cc_final: 0.8265 (tt) REVERT: A 765 GLN cc_start: 0.7935 (mp10) cc_final: 0.7646 (mp10) REVERT: A 768 ARG cc_start: 0.8497 (mtt180) cc_final: 0.7723 (mtt90) REVERT: A 822 MET cc_start: 0.7621 (ptm) cc_final: 0.7221 (pmm) REVERT: A 823 HIS cc_start: 0.7776 (m90) cc_final: 0.7451 (m90) REVERT: A 997 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7269 (m110) REVERT: A 1019 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6322 (tm-30) REVERT: A 1226 MET cc_start: 0.7483 (mmt) cc_final: 0.7176 (mmp) outliers start: 54 outliers final: 38 residues processed: 193 average time/residue: 0.1923 time to fit residues: 51.1847 Evaluate side-chains 175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1222 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 69 optimal weight: 6.9990 chunk 85 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A 820 HIS ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.164973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122257 restraints weight = 11916.312| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.36 r_work: 0.3535 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8101 Z= 0.201 Angle : 0.605 9.724 10995 Z= 0.311 Chirality : 0.039 0.157 1293 Planarity : 0.004 0.053 1349 Dihedral : 8.249 65.503 1099 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 6.67 % Allowed : 26.67 % Favored : 66.67 % 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: 0.33 (0.27), residues: 984 helix: 0.86 (0.20), residues: 675 sheet: -0.65 (1.21), residues: 20 loop : -1.13 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 456 HIS 0.011 0.001 HIS A 820 PHE 0.024 0.002 PHE A 633 TYR 0.019 0.002 TYR A 845 ARG 0.004 0.000 ARG A1205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5476 (OUTLIER) cc_final: 0.4689 (ttt180) REVERT: A 107 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: A 138 LEU cc_start: 0.8396 (mp) cc_final: 0.7598 (tt) REVERT: A 148 GLN cc_start: 0.5833 (OUTLIER) cc_final: 0.5021 (tp40) REVERT: A 177 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5517 (tt) REVERT: A 227 TRP cc_start: 0.7074 (m-10) cc_final: 0.6769 (m-10) REVERT: A 259 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7307 (ttp80) REVERT: A 311 MET cc_start: 0.6157 (mtm) cc_final: 0.5645 (mmt) REVERT: A 320 MET cc_start: 0.6620 (mmt) cc_final: 0.6334 (tpp) REVERT: A 324 LYS cc_start: 0.7373 (mtmt) cc_final: 0.7042 (mttp) REVERT: A 620 ASP cc_start: 0.7366 (t0) cc_final: 0.6899 (p0) REVERT: A 621 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7666 (p0) REVERT: A 646 TRP cc_start: 0.8122 (t-100) cc_final: 0.7667 (t-100) REVERT: A 712 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7603 (m110) REVERT: A 739 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7789 (tt) REVERT: A 765 GLN cc_start: 0.7955 (mp10) cc_final: 0.7508 (mp10) REVERT: A 768 ARG cc_start: 0.8518 (mtt180) cc_final: 0.8129 (mtt90) REVERT: A 813 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7729 (mtpt) REVERT: A 822 MET cc_start: 0.7629 (ptm) cc_final: 0.7216 (pmm) REVERT: A 823 HIS cc_start: 0.7769 (m90) cc_final: 0.7422 (m90) REVERT: A 824 PHE cc_start: 0.6831 (m-80) cc_final: 0.6519 (m-10) REVERT: A 1097 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7344 (pp30) outliers start: 59 outliers final: 36 residues processed: 187 average time/residue: 0.1888 time to fit residues: 48.8988 Evaluate side-chains 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1238 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.159798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.116367 restraints weight = 12131.697| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.38 r_work: 0.3459 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8101 Z= 0.321 Angle : 0.663 8.918 10995 Z= 0.343 Chirality : 0.042 0.148 1293 Planarity : 0.004 0.046 1349 Dihedral : 7.944 63.913 1093 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 7.34 % Allowed : 25.99 % Favored : 66.67 % 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: 0.09 (0.27), residues: 984 helix: 0.67 (0.20), residues: 675 sheet: -1.53 (0.96), residues: 28 loop : -1.10 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 456 HIS 0.003 0.001 HIS A1042 PHE 0.026 0.002 PHE A1240 TYR 0.015 0.002 TYR A1160 ARG 0.005 0.001 ARG A1205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 131 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.4834 (ttt-90) REVERT: A 107 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: A 138 LEU cc_start: 0.8409 (mp) cc_final: 0.7592 (tt) REVERT: A 148 GLN cc_start: 0.6059 (OUTLIER) cc_final: 0.5123 (tp-100) REVERT: A 177 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5701 (tt) REVERT: A 227 TRP cc_start: 0.7082 (m-10) cc_final: 0.6812 (m-10) REVERT: A 259 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7351 (ttp80) REVERT: A 311 MET cc_start: 0.6529 (mtm) cc_final: 0.5946 (mmt) REVERT: A 320 MET cc_start: 0.6712 (mmt) cc_final: 0.6268 (tpp) REVERT: A 324 LYS cc_start: 0.7473 (mtmt) cc_final: 0.7011 (mttp) REVERT: A 367 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4909 (mp) REVERT: A 620 ASP cc_start: 0.7142 (t0) cc_final: 0.6777 (p0) REVERT: A 621 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7672 (p0) REVERT: A 646 TRP cc_start: 0.8130 (t-100) cc_final: 0.7619 (t-100) REVERT: A 712 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7636 (m110) REVERT: A 739 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7955 (tt) REVERT: A 765 GLN cc_start: 0.8019 (mp10) cc_final: 0.7659 (mp10) REVERT: A 820 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.7700 (t-90) REVERT: A 822 MET cc_start: 0.7675 (ptm) cc_final: 0.7278 (pmm) REVERT: A 823 HIS cc_start: 0.7826 (m90) cc_final: 0.7551 (m90) REVERT: A 824 PHE cc_start: 0.6970 (m-80) cc_final: 0.6647 (m-10) REVERT: A 1236 ASP cc_start: 0.7714 (p0) cc_final: 0.7513 (p0) outliers start: 65 outliers final: 44 residues processed: 180 average time/residue: 0.1688 time to fit residues: 42.8033 Evaluate side-chains 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1234 SER Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.156380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112897 restraints weight = 12356.555| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.37 r_work: 0.3406 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 8101 Z= 0.416 Angle : 0.728 10.280 10995 Z= 0.377 Chirality : 0.044 0.161 1293 Planarity : 0.005 0.043 1349 Dihedral : 7.968 63.860 1091 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 7.80 % Allowed : 26.67 % Favored : 65.54 % 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: -0.34 (0.26), residues: 984 helix: 0.36 (0.20), residues: 683 sheet: -1.72 (0.94), residues: 28 loop : -1.37 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 456 HIS 0.003 0.001 HIS A 439 PHE 0.027 0.002 PHE A1240 TYR 0.015 0.002 TYR A 172 ARG 0.005 0.001 ARG A1205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 127 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5740 (OUTLIER) cc_final: 0.4917 (ttt-90) REVERT: A 107 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: A 138 LEU cc_start: 0.8457 (mp) cc_final: 0.7612 (tt) REVERT: A 148 GLN cc_start: 0.6092 (OUTLIER) cc_final: 0.4983 (tp-100) REVERT: A 177 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5901 (tt) REVERT: A 227 TRP cc_start: 0.7163 (m-10) cc_final: 0.6917 (m-10) REVERT: A 257 LEU cc_start: 0.5228 (OUTLIER) cc_final: 0.4899 (tp) REVERT: A 259 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7334 (ttp80) REVERT: A 311 MET cc_start: 0.6545 (mtm) cc_final: 0.5957 (mmt) REVERT: A 320 MET cc_start: 0.6830 (mmt) cc_final: 0.6371 (tpp) REVERT: A 324 LYS cc_start: 0.7594 (mtmt) cc_final: 0.7129 (mttp) REVERT: A 367 LEU cc_start: 0.5266 (OUTLIER) cc_final: 0.5045 (mp) REVERT: A 393 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6477 (ttm170) REVERT: A 620 ASP cc_start: 0.7342 (t0) cc_final: 0.7023 (p0) REVERT: A 621 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7771 (p0) REVERT: A 646 TRP cc_start: 0.8151 (t-100) cc_final: 0.7636 (t-100) REVERT: A 712 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7570 (m110) REVERT: A 765 GLN cc_start: 0.8097 (mp10) cc_final: 0.7724 (mp10) REVERT: A 804 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7376 (mt) REVERT: A 822 MET cc_start: 0.7761 (ptm) cc_final: 0.7269 (pmm) REVERT: A 823 HIS cc_start: 0.7858 (m90) cc_final: 0.7537 (m-70) REVERT: A 824 PHE cc_start: 0.7100 (m-80) cc_final: 0.6664 (m-10) outliers start: 69 outliers final: 50 residues processed: 182 average time/residue: 0.1915 time to fit residues: 48.9765 Evaluate side-chains 180 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 120 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1234 SER Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 71 optimal weight: 0.0980 chunk 72 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.163621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120338 restraints weight = 12149.692| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.40 r_work: 0.3513 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8101 Z= 0.179 Angle : 0.589 12.210 10995 Z= 0.298 Chirality : 0.039 0.150 1293 Planarity : 0.004 0.043 1349 Dihedral : 7.581 59.710 1091 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 5.42 % Allowed : 29.94 % Favored : 64.63 % 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: 0.19 (0.27), residues: 984 helix: 0.78 (0.20), residues: 676 sheet: -2.16 (0.69), residues: 48 loop : -0.96 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 208 HIS 0.002 0.000 HIS A1042 PHE 0.023 0.001 PHE A 986 TYR 0.015 0.001 TYR A1160 ARG 0.004 0.000 ARG A1205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.4834 (ttt-90) REVERT: A 107 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: A 138 LEU cc_start: 0.8303 (mp) cc_final: 0.7543 (tt) REVERT: A 148 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5132 (tp40) REVERT: A 177 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5938 (tt) REVERT: A 227 TRP cc_start: 0.7003 (m-10) cc_final: 0.6785 (m-10) REVERT: A 246 MET cc_start: 0.7338 (tmm) cc_final: 0.7111 (tmm) REVERT: A 259 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7329 (ttp80) REVERT: A 311 MET cc_start: 0.6300 (mtm) cc_final: 0.5765 (mmt) REVERT: A 320 MET cc_start: 0.6791 (mmt) cc_final: 0.6539 (tpp) REVERT: A 324 LYS cc_start: 0.7445 (mtmt) cc_final: 0.7122 (mttp) REVERT: A 620 ASP cc_start: 0.7543 (t0) cc_final: 0.7124 (p0) REVERT: A 621 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7695 (p0) REVERT: A 646 TRP cc_start: 0.8111 (t-100) cc_final: 0.7591 (t-100) REVERT: A 712 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7639 (m110) REVERT: A 765 GLN cc_start: 0.8075 (mp10) cc_final: 0.7602 (mp10) REVERT: A 768 ARG cc_start: 0.8848 (mtt180) cc_final: 0.8242 (mtt90) REVERT: A 813 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7365 (mtpp) REVERT: A 820 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7697 (t-170) REVERT: A 822 MET cc_start: 0.7665 (ptm) cc_final: 0.7255 (pmm) REVERT: A 823 HIS cc_start: 0.7849 (m90) cc_final: 0.7613 (m90) REVERT: A 824 PHE cc_start: 0.7096 (m-80) cc_final: 0.6598 (m-10) outliers start: 48 outliers final: 34 residues processed: 173 average time/residue: 0.1982 time to fit residues: 47.5935 Evaluate side-chains 163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1234 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.161570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118069 restraints weight = 12233.441| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.40 r_work: 0.3479 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8101 Z= 0.229 Angle : 0.610 11.938 10995 Z= 0.307 Chirality : 0.039 0.148 1293 Planarity : 0.004 0.046 1349 Dihedral : 7.377 58.759 1088 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.88 % Allowed : 29.27 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.27), residues: 984 helix: 0.81 (0.20), residues: 682 sheet: -2.23 (0.67), residues: 48 loop : -1.09 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 456 HIS 0.002 0.000 HIS A 692 PHE 0.022 0.001 PHE A1240 TYR 0.019 0.002 TYR A 845 ARG 0.003 0.000 ARG A1205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5617 (OUTLIER) cc_final: 0.4846 (ttt-90) REVERT: A 107 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: A 121 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7180 (tpt90) REVERT: A 138 LEU cc_start: 0.8300 (mp) cc_final: 0.7505 (tt) REVERT: A 148 GLN cc_start: 0.5982 (OUTLIER) cc_final: 0.5041 (tp-100) REVERT: A 177 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5983 (tt) REVERT: A 227 TRP cc_start: 0.7043 (m-10) cc_final: 0.6803 (m-10) REVERT: A 259 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7325 (ttp80) REVERT: A 311 MET cc_start: 0.6435 (mtm) cc_final: 0.5960 (mmt) REVERT: A 320 MET cc_start: 0.7057 (mmt) cc_final: 0.6809 (tpp) REVERT: A 324 LYS cc_start: 0.7447 (mtmt) cc_final: 0.7205 (mttp) REVERT: A 620 ASP cc_start: 0.7478 (t0) cc_final: 0.7119 (p0) REVERT: A 621 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7764 (p0) REVERT: A 646 TRP cc_start: 0.8166 (t-100) cc_final: 0.7686 (t-100) REVERT: A 712 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7664 (m110) REVERT: A 765 GLN cc_start: 0.8120 (mp10) cc_final: 0.7712 (mp10) REVERT: A 768 ARG cc_start: 0.8879 (mtt180) cc_final: 0.8260 (mtt90) REVERT: A 813 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7325 (mtpp) REVERT: A 822 MET cc_start: 0.7705 (ptm) cc_final: 0.7264 (pmm) REVERT: A 823 HIS cc_start: 0.7871 (m90) cc_final: 0.7655 (t-90) REVERT: A 824 PHE cc_start: 0.7168 (m-80) cc_final: 0.6266 (m-10) outliers start: 52 outliers final: 39 residues processed: 171 average time/residue: 0.1951 time to fit residues: 46.2222 Evaluate side-chains 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1234 SER Chi-restraints excluded: chain A residue 1244 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 0.0170 chunk 86 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.166315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123105 restraints weight = 12171.547| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.30 r_work: 0.3552 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8101 Z= 0.196 Angle : 0.587 11.920 10995 Z= 0.295 Chirality : 0.039 0.160 1293 Planarity : 0.004 0.046 1349 Dihedral : 7.304 59.582 1088 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.20 % Allowed : 30.28 % Favored : 64.52 % 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: 0.37 (0.27), residues: 984 helix: 0.96 (0.21), residues: 682 sheet: -2.24 (0.64), residues: 48 loop : -1.04 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 358 HIS 0.002 0.001 HIS A 798 PHE 0.023 0.001 PHE A1240 TYR 0.017 0.001 TYR A1160 ARG 0.003 0.000 ARG A1205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.4725 (ttt-90) REVERT: A 107 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: A 121 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7212 (tpt90) REVERT: A 138 LEU cc_start: 0.8280 (mp) cc_final: 0.7520 (tt) REVERT: A 148 GLN cc_start: 0.5940 (OUTLIER) cc_final: 0.5054 (tp40) REVERT: A 177 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5958 (tt) REVERT: A 227 TRP cc_start: 0.6999 (m-10) cc_final: 0.6772 (m-10) REVERT: A 259 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7325 (ttp80) REVERT: A 311 MET cc_start: 0.6399 (mtm) cc_final: 0.5923 (mmt) REVERT: A 320 MET cc_start: 0.7247 (mmt) cc_final: 0.7036 (tpp) REVERT: A 324 LYS cc_start: 0.7484 (mtmt) cc_final: 0.7234 (mttp) REVERT: A 620 ASP cc_start: 0.7475 (t0) cc_final: 0.7156 (p0) REVERT: A 646 TRP cc_start: 0.8072 (t-100) cc_final: 0.7547 (t-100) REVERT: A 765 GLN cc_start: 0.8114 (mp10) cc_final: 0.7622 (mp10) REVERT: A 768 ARG cc_start: 0.8866 (mtt180) cc_final: 0.8241 (mtt90) REVERT: A 820 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.7802 (t-90) REVERT: A 822 MET cc_start: 0.7687 (ptm) cc_final: 0.7245 (pmm) REVERT: A 824 PHE cc_start: 0.7264 (m-80) cc_final: 0.6596 (m-10) outliers start: 46 outliers final: 37 residues processed: 166 average time/residue: 0.1851 time to fit residues: 42.5596 Evaluate side-chains 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 72 optimal weight: 0.0470 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 HIS A 997 ASN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.165825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122308 restraints weight = 12249.333| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.35 r_work: 0.3555 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8101 Z= 0.209 Angle : 0.611 12.020 10995 Z= 0.305 Chirality : 0.039 0.187 1293 Planarity : 0.004 0.046 1349 Dihedral : 7.124 59.163 1084 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.42 % Allowed : 29.72 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 984 helix: 1.02 (0.21), residues: 679 sheet: -2.29 (0.62), residues: 48 loop : -1.00 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 358 HIS 0.006 0.001 HIS A 823 PHE 0.023 0.001 PHE A1240 TYR 0.020 0.002 TYR A 845 ARG 0.004 0.000 ARG A 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5572 (OUTLIER) cc_final: 0.4767 (ttt-90) REVERT: A 107 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: A 121 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7237 (tpt90) REVERT: A 138 LEU cc_start: 0.8313 (mp) cc_final: 0.7555 (tt) REVERT: A 148 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.5061 (tp-100) REVERT: A 177 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5905 (tt) REVERT: A 227 TRP cc_start: 0.7026 (m-10) cc_final: 0.6796 (m-10) REVERT: A 259 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7359 (ttp80) REVERT: A 311 MET cc_start: 0.6426 (mtm) cc_final: 0.5950 (mmt) REVERT: A 320 MET cc_start: 0.7265 (mmt) cc_final: 0.7014 (tpp) REVERT: A 324 LYS cc_start: 0.7508 (mtmt) cc_final: 0.7263 (mttp) REVERT: A 620 ASP cc_start: 0.7493 (t0) cc_final: 0.7186 (p0) REVERT: A 646 TRP cc_start: 0.8114 (t-100) cc_final: 0.7624 (t-100) REVERT: A 765 GLN cc_start: 0.8080 (mp10) cc_final: 0.7606 (mp10) REVERT: A 768 ARG cc_start: 0.8875 (mtt180) cc_final: 0.8269 (mtt90) REVERT: A 797 LYS cc_start: 0.8121 (tptm) cc_final: 0.7907 (tptp) REVERT: A 820 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7721 (t-90) REVERT: A 822 MET cc_start: 0.7605 (ptm) cc_final: 0.7228 (pmm) REVERT: A 824 PHE cc_start: 0.7040 (m-80) cc_final: 0.6396 (m-10) outliers start: 48 outliers final: 39 residues processed: 164 average time/residue: 0.1820 time to fit residues: 41.8768 Evaluate side-chains 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 4.9990 chunk 59 optimal weight: 0.0040 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.167972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124733 restraints weight = 11972.730| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.28 r_work: 0.3578 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8101 Z= 0.186 Angle : 0.598 11.970 10995 Z= 0.299 Chirality : 0.039 0.195 1293 Planarity : 0.004 0.046 1349 Dihedral : 7.045 59.119 1084 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.20 % Allowed : 29.60 % Favored : 65.20 % 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: 0.50 (0.27), residues: 984 helix: 1.12 (0.21), residues: 682 sheet: -2.35 (0.61), residues: 48 loop : -1.16 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.000 HIS A 820 PHE 0.023 0.001 PHE A1240 TYR 0.013 0.001 TYR A 209 ARG 0.004 0.000 ARG A 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4405.21 seconds wall clock time: 78 minutes 37.46 seconds (4717.46 seconds total)