Starting phenix.real_space_refine on Fri Feb 16 18:53:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/02_2024/7q62_13850.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/02_2024/7q62_13850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/02_2024/7q62_13850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/02_2024/7q62_13850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/02_2024/7q62_13850.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q62_13850/02_2024/7q62_13850.pdb" } resolution = 3.18 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= 0.005 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 75 5.16 5 C 10356 2.51 5 N 2653 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16186 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9560 Classifications: {'peptide': 1223} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1159} Chain breaks: 3 Chain: "B" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6486 Classifications: {'peptide': 822} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 772} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 9.28, per 1000 atoms: 0.57 Number of scatterers: 16186 At special positions: 0 Unit cell: (106.108, 122.93, 142.34, 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 75 16.00 O 3102 8.00 N 2653 7.00 C 10356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.02 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.11 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.02 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 78 " distance=2.02 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 291 " distance=2.04 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 589 " - pdb=" SG CYS B 769 " distance=2.02 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 694 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B 845 " - pdb=" SG CYS B 881 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1501 " - " ASN A 120 " " NAG A1502 " - " ASN A 328 " " NAG A1503 " - " ASN A 609 " " NAG A1504 " - " ASN A 857 " " NAG A1505 " - " ASN A 867 " " NAG B1501 " - " ASN B 120 " " NAG B1502 " - " ASN B 328 " " NAG B1503 " - " ASN B 609 " " NAG B1504 " - " ASN B 857 " " NAG B1505 " - " ASN B 867 " Time building additional restraints: 7.37 Conformation dependent library (CDL) restraints added in 3.0 seconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 34 sheets defined 12.2% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 406 through 409 removed outlier: 4.133A pdb=" N ASN A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 597 through 602 removed outlier: 4.008A pdb=" N LEU A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 597 through 602' Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 670 through 679 removed outlier: 3.674A pdb=" N VAL A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 963 removed outlier: 3.704A pdb=" N LEU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 979 removed outlier: 4.343A pdb=" N VAL A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 990 removed outlier: 4.265A pdb=" N TYR A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 990 " --> pdb=" O GLN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1010 Processing helix chain 'A' and resid 1011 through 1014 Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1056 through 1070 removed outlier: 3.845A pdb=" N LYS A1064 " --> pdb=" O GLN A1060 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TRP A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1104 removed outlier: 3.612A pdb=" N LEU A1097 " --> pdb=" O ASP A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 4.294A pdb=" N MET A1108 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A1109 " --> pdb=" O LEU A1106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1109' Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 4.331A pdb=" N ASN A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A1127 " --> pdb=" O CYS A1123 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1129 " --> pdb=" O LYS A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1148 removed outlier: 3.796A pdb=" N ILE A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1162 removed outlier: 3.946A pdb=" N LYS A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN A1159 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A1162 " --> pdb=" O LYS A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1207 removed outlier: 3.702A pdb=" N LYS A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1227 removed outlier: 4.039A pdb=" N LYS A1227 " --> pdb=" O ALA A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 removed outlier: 3.552A pdb=" N ALA A1255 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 removed outlier: 3.824A pdb=" N ALA B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 478 through 481' Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.807A pdb=" N LYS B 511 " --> pdb=" O ASN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 602 removed outlier: 3.719A pdb=" N LEU B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 624 through 628 removed outlier: 3.697A pdb=" N ALA B 628 " --> pdb=" O TYR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82 removed outlier: 8.244A pdb=" N LYS A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.797A pdb=" N PHE A 52 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU A 67 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 54 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.759A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 346 removed outlier: 4.038A pdb=" N GLU A 345 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS A 360 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 455 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 507 removed outlier: 5.308A pdb=" N LEU A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 495 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 487 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB4, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB5, first strand: chain 'A' and resid 790 through 795 Processing sheet with id=AB6, first strand: chain 'A' and resid 800 through 801 removed outlier: 7.081A pdb=" N VAL A 800 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 908 through 918 Processing sheet with id=AB8, first strand: chain 'A' and resid 921 through 930 Processing sheet with id=AB9, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.599A pdb=" N TYR A1172 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 75 through 82 removed outlier: 8.101A pdb=" N LYS B 38 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.814A pdb=" N LEU B 56 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS B 64 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 121 through 126 Processing sheet with id=AC4, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.626A pdb=" N SER B 156 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU B 172 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN B 170 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 160 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 219 through 223 Processing sheet with id=AC6, first strand: chain 'B' and resid 229 through 230 removed outlier: 6.230A pdb=" N LEU B 229 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS B 310 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN B 311 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS B 261 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 340 through 346 removed outlier: 5.431A pdb=" N MET B 342 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ARG B 364 " --> pdb=" O MET B 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 344 " --> pdb=" O ARG B 362 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 362 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 346 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AC9, first strand: chain 'B' and resid 451 through 455 Processing sheet with id=AD1, first strand: chain 'B' and resid 498 through 507 removed outlier: 5.152A pdb=" N LEU B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY B 495 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER B 488 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE B 539 " --> pdb=" O SER B 488 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 563 through 567 Processing sheet with id=AD3, first strand: chain 'B' and resid 742 through 743 Processing sheet with id=AD4, first strand: chain 'B' and resid 592 through 595 Processing sheet with id=AD5, first strand: chain 'B' and resid 729 through 730 removed outlier: 5.938A pdb=" N VAL B 800 " --> pdb=" O LYS B 904 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD7, first strand: chain 'B' and resid 790 through 795 640 hydrogen bonds defined for protein. 1758 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: 7.61 Time building geometry restraints manager: 7.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5061 1.34 - 1.46: 4006 1.46 - 1.59: 7390 1.59 - 1.71: 0 1.71 - 1.84: 110 Bond restraints: 16567 Sorted by residual: bond pdb=" CD GLU B 596 " pdb=" OE1 GLU B 596 " ideal model delta sigma weight residual 1.249 1.326 -0.077 1.90e-02 2.77e+03 1.66e+01 bond pdb=" CD GLU A 596 " pdb=" OE1 GLU A 596 " ideal model delta sigma weight residual 1.249 1.321 -0.072 1.90e-02 2.77e+03 1.45e+01 bond pdb=" N ILE A1318 " pdb=" CA ILE A1318 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.61e+00 bond pdb=" N GLY A1031 " pdb=" CA GLY A1031 " ideal model delta sigma weight residual 1.449 1.478 -0.028 9.80e-03 1.04e+04 8.41e+00 bond pdb=" C1 NAG A1504 " pdb=" O5 NAG A1504 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.36e+00 ... (remaining 16562 not shown) Histogram of bond angle deviations from ideal: 97.69 - 108.53: 1174 108.53 - 119.38: 12690 119.38 - 130.22: 8575 130.22 - 141.06: 73 141.06 - 151.91: 2 Bond angle restraints: 22514 Sorted by residual: angle pdb=" CA CYS A 279 " pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " ideal model delta sigma weight residual 114.40 151.91 -37.51 2.30e+00 1.89e-01 2.66e+02 angle pdb=" CA CYS A 259 " pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " ideal model delta sigma weight residual 114.40 151.66 -37.26 2.30e+00 1.89e-01 2.62e+02 angle pdb=" N CYS A 259 " pdb=" CA CYS A 259 " pdb=" C CYS A 259 " ideal model delta sigma weight residual 108.99 122.76 -13.77 1.57e+00 4.06e-01 7.69e+01 angle pdb=" N CYS A 279 " pdb=" CA CYS A 279 " pdb=" C CYS A 279 " ideal model delta sigma weight residual 108.79 119.95 -11.16 1.53e+00 4.27e-01 5.32e+01 angle pdb=" C ASN B 103 " pdb=" N ASN B 104 " pdb=" CA ASN B 104 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 ... (remaining 22509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 9123 17.69 - 35.38: 733 35.38 - 53.07: 137 53.07 - 70.76: 39 70.76 - 88.45: 34 Dihedral angle restraints: 10066 sinusoidal: 4126 harmonic: 5940 Sorted by residual: dihedral pdb=" CB CYS A 633 " pdb=" SG CYS A 633 " pdb=" SG CYS A 694 " pdb=" CB CYS A 694 " ideal model delta sinusoidal sigma weight residual -86.00 -173.78 87.78 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual -86.00 -2.50 -83.50 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CA GLU A 835 " pdb=" C GLU A 835 " pdb=" N SER A 836 " pdb=" CA SER A 836 " ideal model delta harmonic sigma weight residual 180.00 140.64 39.36 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 10063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2446 0.139 - 0.277: 93 0.277 - 0.416: 10 0.416 - 0.554: 3 0.554 - 0.693: 1 Chirality restraints: 2553 Sorted by residual: chirality pdb=" C1 NAG A1504 " pdb=" ND2 ASN A 857 " pdb=" C2 NAG A1504 " pdb=" O5 NAG A1504 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA CYS A 259 " pdb=" N CYS A 259 " pdb=" C CYS A 259 " pdb=" CB CYS A 259 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CA CYS A 279 " pdb=" N CYS A 279 " pdb=" C CYS A 279 " pdb=" CB CYS A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 2550 not shown) Planarity restraints: 2899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 837 " 0.029 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP A 837 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 837 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 837 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 837 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 837 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 837 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 837 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 837 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 837 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 44 " 0.057 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A 45 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 609 " 0.027 2.00e-02 2.50e+03 2.64e-02 8.73e+00 pdb=" CG ASN B 609 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 609 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 609 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG B1503 " 0.030 2.00e-02 2.50e+03 ... (remaining 2896 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4033 2.80 - 3.33: 13141 3.33 - 3.85: 26931 3.85 - 4.38: 29959 4.38 - 4.90: 52543 Nonbonded interactions: 126607 Sorted by model distance: nonbonded pdb=" OD1 ASP A 127 " pdb=" OH TYR A 131 " model vdw 2.276 2.440 nonbonded pdb=" O ALA B 827 " pdb=" OH TYR B 832 " model vdw 2.327 2.440 nonbonded pdb=" O ALA A 827 " pdb=" OH TYR A 832 " model vdw 2.333 2.440 nonbonded pdb=" OD1 ASP B 127 " pdb=" OH TYR B 131 " model vdw 2.337 2.440 nonbonded pdb=" OG1 THR A1238 " pdb=" OE1 GLN A1239 " model vdw 2.341 2.440 ... (remaining 126602 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: 7.610 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: 28.130 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 48.940 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.006 0.092 16567 Z= 0.372 Angle : 1.133 37.509 22514 Z= 0.569 Chirality : 0.067 0.693 2553 Planarity : 0.008 0.105 2889 Dihedral : 14.476 88.447 6200 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 0.06 % Allowed : 0.67 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.17), residues: 2031 helix: -2.90 (0.26), residues: 204 sheet: -0.24 (0.17), residues: 917 loop : -1.65 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A 837 HIS 0.007 0.001 HIS A 77 PHE 0.030 0.003 PHE A1286 TYR 0.049 0.003 TYR B 306 ARG 0.022 0.001 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.997 Fit side-chains REVERT: A 266 TRP cc_start: 0.6368 (m-10) cc_final: 0.6051 (m-90) REVERT: A 394 ASP cc_start: 0.7663 (p0) cc_final: 0.7412 (p0) REVERT: A 578 GLU cc_start: 0.7945 (tt0) cc_final: 0.7547 (tt0) REVERT: A 985 LEU cc_start: 0.9067 (mm) cc_final: 0.8834 (mm) REVERT: A 1015 MET cc_start: 0.7157 (pmm) cc_final: 0.6045 (tmm) REVERT: A 1065 TRP cc_start: 0.6221 (m100) cc_final: 0.5448 (m100) REVERT: A 1173 TRP cc_start: 0.6464 (m-90) cc_final: 0.5897 (m-90) REVERT: A 1297 MET cc_start: 0.7573 (pmm) cc_final: 0.7273 (pmm) REVERT: B 298 MET cc_start: 0.7019 (ppp) cc_final: 0.6725 (ppp) REVERT: B 306 TYR cc_start: 0.7928 (t80) cc_final: 0.7713 (t80) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2486 time to fit residues: 70.8285 Evaluate side-chains 133 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 159 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 119 optimal weight: 0.0770 chunk 185 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 352 HIS A 504 GLN A 506 HIS B 22 ASN B 164 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16567 Z= 0.181 Angle : 0.632 16.717 22514 Z= 0.316 Chirality : 0.046 0.534 2553 Planarity : 0.005 0.054 2889 Dihedral : 6.193 57.845 2402 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 0.67 % Allowed : 7.10 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.16 (0.18), residues: 2031 helix: -1.57 (0.30), residues: 217 sheet: -0.09 (0.17), residues: 908 loop : -1.19 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 837 HIS 0.004 0.001 HIS A 77 PHE 0.037 0.001 PHE A1286 TYR 0.016 0.001 TYR B 491 ARG 0.005 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 2.097 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6430 (m-10) cc_final: 0.6054 (m-90) REVERT: A 394 ASP cc_start: 0.7701 (p0) cc_final: 0.7395 (p0) REVERT: A 578 GLU cc_start: 0.7939 (tt0) cc_final: 0.7428 (tt0) REVERT: A 619 TRP cc_start: 0.5842 (p90) cc_final: 0.5461 (p-90) REVERT: A 985 LEU cc_start: 0.9052 (mm) cc_final: 0.8765 (mm) REVERT: A 1065 TRP cc_start: 0.6004 (m100) cc_final: 0.5342 (m100) REVERT: A 1142 TYR cc_start: 0.9001 (t80) cc_final: 0.8735 (t80) REVERT: A 1288 GLN cc_start: 0.7873 (mp-120) cc_final: 0.7619 (mm110) REVERT: B 157 MET cc_start: 0.7854 (ppp) cc_final: 0.7364 (ppp) REVERT: B 298 MET cc_start: 0.7161 (ppp) cc_final: 0.6824 (ppp) REVERT: B 387 PHE cc_start: 0.9087 (t80) cc_final: 0.8865 (t80) outliers start: 12 outliers final: 7 residues processed: 147 average time/residue: 0.2482 time to fit residues: 58.7540 Evaluate side-chains 136 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 472 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16567 Z= 0.223 Angle : 0.618 16.210 22514 Z= 0.307 Chirality : 0.045 0.506 2553 Planarity : 0.004 0.055 2889 Dihedral : 5.787 55.424 2402 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.17 % Rotamer: Outliers : 1.12 % Allowed : 9.00 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.18), residues: 2031 helix: -0.64 (0.33), residues: 215 sheet: -0.03 (0.17), residues: 912 loop : -0.97 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1173 HIS 0.003 0.001 HIS A 506 PHE 0.037 0.001 PHE A1286 TYR 0.015 0.001 TYR B 491 ARG 0.004 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.999 Fit side-chains REVERT: A 266 TRP cc_start: 0.6510 (m-10) cc_final: 0.6147 (m-90) REVERT: A 394 ASP cc_start: 0.7760 (p0) cc_final: 0.7483 (p0) REVERT: A 421 MET cc_start: 0.8078 (mmm) cc_final: 0.7779 (mmm) REVERT: A 735 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6500 (mm-30) REVERT: A 985 LEU cc_start: 0.9059 (mm) cc_final: 0.8778 (mm) REVERT: A 1065 TRP cc_start: 0.5932 (m100) cc_final: 0.5272 (m100) REVERT: A 1288 GLN cc_start: 0.7827 (mp-120) cc_final: 0.7606 (mm110) REVERT: B 157 MET cc_start: 0.7948 (ppp) cc_final: 0.7540 (ppp) REVERT: B 298 MET cc_start: 0.7251 (ppp) cc_final: 0.6855 (ppp) REVERT: B 387 PHE cc_start: 0.9110 (t80) cc_final: 0.8843 (t80) REVERT: B 608 SER cc_start: 0.8966 (t) cc_final: 0.8529 (p) outliers start: 20 outliers final: 14 residues processed: 141 average time/residue: 0.2285 time to fit residues: 53.4513 Evaluate side-chains 138 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 0.0040 chunk 124 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 176 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16567 Z= 0.169 Angle : 0.572 11.436 22514 Z= 0.281 Chirality : 0.044 0.511 2553 Planarity : 0.004 0.057 2889 Dihedral : 5.545 55.503 2402 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 1.34 % Allowed : 10.57 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.58 (0.19), residues: 2031 helix: -0.15 (0.34), residues: 215 sheet: 0.05 (0.17), residues: 914 loop : -0.80 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 837 HIS 0.002 0.000 HIS A 506 PHE 0.040 0.001 PHE A1286 TYR 0.015 0.001 TYR B 491 ARG 0.003 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.936 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8854 (pt) REVERT: A 266 TRP cc_start: 0.6527 (m-10) cc_final: 0.6196 (m-90) REVERT: A 394 ASP cc_start: 0.7760 (p0) cc_final: 0.7506 (p0) REVERT: A 421 MET cc_start: 0.8145 (mmm) cc_final: 0.7858 (mmm) REVERT: A 619 TRP cc_start: 0.6784 (p90) cc_final: 0.5952 (p-90) REVERT: A 735 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6485 (mm-30) REVERT: A 985 LEU cc_start: 0.9036 (mm) cc_final: 0.8736 (mm) REVERT: A 1065 TRP cc_start: 0.5975 (m100) cc_final: 0.5333 (m100) REVERT: B 157 MET cc_start: 0.7920 (ppp) cc_final: 0.7564 (ppp) REVERT: B 387 PHE cc_start: 0.9123 (t80) cc_final: 0.8843 (t80) REVERT: B 501 MET cc_start: 0.7957 (ttp) cc_final: 0.7573 (ttm) REVERT: B 591 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8253 (tt) outliers start: 24 outliers final: 18 residues processed: 151 average time/residue: 0.2388 time to fit residues: 59.0346 Evaluate side-chains 143 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1288 GLN B 331 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16567 Z= 0.332 Angle : 0.638 11.267 22514 Z= 0.317 Chirality : 0.045 0.501 2553 Planarity : 0.004 0.058 2889 Dihedral : 5.832 56.294 2402 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 2.40 % Allowed : 11.58 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.58 (0.19), residues: 2031 helix: 0.12 (0.35), residues: 215 sheet: 0.02 (0.17), residues: 902 loop : -0.82 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 837 HIS 0.004 0.001 HIS A 506 PHE 0.013 0.002 PHE B 768 TYR 0.016 0.001 TYR A1142 ARG 0.003 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 1.995 Fit side-chains REVERT: A 266 TRP cc_start: 0.6491 (m-10) cc_final: 0.6204 (m-90) REVERT: A 394 ASP cc_start: 0.7897 (p0) cc_final: 0.7697 (p0) REVERT: A 953 MET cc_start: 0.5337 (ptt) cc_final: 0.5084 (ptt) REVERT: A 973 GLN cc_start: 0.7814 (pm20) cc_final: 0.7538 (pm20) REVERT: A 985 LEU cc_start: 0.9096 (mm) cc_final: 0.8814 (mm) REVERT: A 1015 MET cc_start: 0.7301 (pmm) cc_final: 0.6284 (tmm) REVERT: A 1065 TRP cc_start: 0.5997 (m100) cc_final: 0.5348 (m100) REVERT: A 1288 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7425 (mm110) REVERT: B 157 MET cc_start: 0.8111 (ppp) cc_final: 0.7654 (ppp) REVERT: B 173 GLU cc_start: 0.7525 (tp30) cc_final: 0.7295 (tp30) REVERT: B 387 PHE cc_start: 0.9103 (t80) cc_final: 0.8837 (t80) REVERT: B 501 MET cc_start: 0.8199 (ttp) cc_final: 0.7755 (ttm) REVERT: B 608 SER cc_start: 0.9027 (t) cc_final: 0.8615 (p) outliers start: 43 outliers final: 29 residues processed: 162 average time/residue: 0.2360 time to fit residues: 62.3635 Evaluate side-chains 152 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16567 Z= 0.270 Angle : 0.626 11.110 22514 Z= 0.310 Chirality : 0.045 0.505 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.772 57.924 2402 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.35 % Allowed : 12.64 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.52 (0.19), residues: 2031 helix: 0.24 (0.35), residues: 215 sheet: -0.03 (0.17), residues: 913 loop : -0.70 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 837 HIS 0.003 0.001 HIS A 506 PHE 0.013 0.001 PHE B 887 TYR 0.021 0.001 TYR B 68 ARG 0.002 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 1.734 Fit side-chains REVERT: A 266 TRP cc_start: 0.6514 (m-10) cc_final: 0.6226 (m-90) REVERT: A 985 LEU cc_start: 0.9082 (mm) cc_final: 0.8801 (mm) REVERT: A 1065 TRP cc_start: 0.5972 (m100) cc_final: 0.5337 (m100) REVERT: A 1173 TRP cc_start: 0.6598 (m-90) cc_final: 0.6012 (m-90) REVERT: A 1288 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7670 (mm110) REVERT: B 157 MET cc_start: 0.8056 (ppp) cc_final: 0.7618 (ppp) REVERT: B 173 GLU cc_start: 0.7436 (tp30) cc_final: 0.7226 (tp30) REVERT: B 387 PHE cc_start: 0.9104 (t80) cc_final: 0.8873 (t80) REVERT: B 501 MET cc_start: 0.8178 (ttp) cc_final: 0.7753 (ttm) REVERT: B 608 SER cc_start: 0.9005 (t) cc_final: 0.8615 (p) outliers start: 42 outliers final: 31 residues processed: 158 average time/residue: 0.2499 time to fit residues: 65.4248 Evaluate side-chains 151 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16567 Z= 0.228 Angle : 0.611 11.002 22514 Z= 0.300 Chirality : 0.045 0.508 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.692 56.918 2402 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.63 % Allowed : 12.98 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.48 (0.19), residues: 2031 helix: 0.27 (0.35), residues: 217 sheet: 0.04 (0.17), residues: 907 loop : -0.73 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 837 HIS 0.004 0.001 HIS B 506 PHE 0.014 0.001 PHE B 887 TYR 0.018 0.001 TYR B 68 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 121 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6562 (m-10) cc_final: 0.6282 (m-90) REVERT: A 985 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8799 (mm) REVERT: A 1015 MET cc_start: 0.7274 (pmm) cc_final: 0.6287 (tmm) REVERT: A 1065 TRP cc_start: 0.5947 (m100) cc_final: 0.5310 (m100) REVERT: A 1173 TRP cc_start: 0.6579 (m-90) cc_final: 0.6036 (m-90) REVERT: A 1288 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7720 (mm110) REVERT: A 1298 TYR cc_start: 0.7698 (m-80) cc_final: 0.7248 (m-80) REVERT: B 67 GLU cc_start: 0.6733 (tp30) cc_final: 0.6401 (tp30) REVERT: B 157 MET cc_start: 0.8027 (ppp) cc_final: 0.7589 (ppp) REVERT: B 387 PHE cc_start: 0.9110 (t80) cc_final: 0.8891 (t80) REVERT: B 501 MET cc_start: 0.8122 (ttp) cc_final: 0.7669 (ttm) REVERT: B 608 SER cc_start: 0.8983 (t) cc_final: 0.8589 (p) outliers start: 47 outliers final: 37 residues processed: 159 average time/residue: 0.2265 time to fit residues: 60.0995 Evaluate side-chains 156 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 0.0060 chunk 154 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16567 Z= 0.180 Angle : 0.602 10.885 22514 Z= 0.293 Chirality : 0.045 0.507 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.494 55.519 2402 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.18 % Allowed : 13.81 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.38 (0.19), residues: 2031 helix: 0.37 (0.35), residues: 217 sheet: 0.13 (0.17), residues: 899 loop : -0.70 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 837 HIS 0.003 0.000 HIS A 753 PHE 0.013 0.001 PHE B 887 TYR 0.015 0.001 TYR B 68 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 1.993 Fit side-chains revert: symmetry clash REVERT: A 735 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6605 (mm-30) REVERT: A 985 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8781 (mm) REVERT: A 1015 MET cc_start: 0.7281 (pmm) cc_final: 0.6251 (tmm) REVERT: A 1065 TRP cc_start: 0.5956 (m100) cc_final: 0.5323 (m100) REVERT: A 1173 TRP cc_start: 0.6515 (m-90) cc_final: 0.6304 (m-90) REVERT: A 1288 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7776 (mm110) REVERT: B 67 GLU cc_start: 0.6715 (tp30) cc_final: 0.6355 (tp30) REVERT: B 157 MET cc_start: 0.7986 (ppp) cc_final: 0.7571 (ppp) REVERT: B 387 PHE cc_start: 0.9109 (t80) cc_final: 0.8836 (t80) REVERT: B 501 MET cc_start: 0.8058 (ttp) cc_final: 0.7592 (ttm) REVERT: B 608 SER cc_start: 0.8929 (t) cc_final: 0.8529 (p) outliers start: 39 outliers final: 36 residues processed: 154 average time/residue: 0.2392 time to fit residues: 61.0986 Evaluate side-chains 154 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 752 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 182 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16567 Z= 0.231 Angle : 0.621 10.870 22514 Z= 0.302 Chirality : 0.045 0.499 2553 Planarity : 0.004 0.060 2889 Dihedral : 5.526 54.949 2402 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.18 % Allowed : 14.15 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 (0.19), residues: 2031 helix: 0.37 (0.35), residues: 217 sheet: 0.10 (0.17), residues: 910 loop : -0.66 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 837 HIS 0.003 0.001 HIS A 753 PHE 0.016 0.001 PHE B 887 TYR 0.016 0.001 TYR B 491 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 1.959 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6515 (m-90) cc_final: 0.5264 (m-10) REVERT: A 735 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6664 (mm-30) REVERT: A 985 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8796 (mm) REVERT: A 1015 MET cc_start: 0.7308 (pmm) cc_final: 0.6292 (tmm) REVERT: A 1065 TRP cc_start: 0.5928 (m100) cc_final: 0.5297 (m100) REVERT: A 1142 TYR cc_start: 0.8949 (t80) cc_final: 0.8732 (t80) REVERT: A 1298 TYR cc_start: 0.7586 (m-80) cc_final: 0.7237 (m-80) REVERT: B 157 MET cc_start: 0.8050 (ppp) cc_final: 0.7624 (ppp) REVERT: B 501 MET cc_start: 0.8168 (ttp) cc_final: 0.7713 (ttm) REVERT: B 608 SER cc_start: 0.8954 (t) cc_final: 0.8570 (p) outliers start: 39 outliers final: 37 residues processed: 152 average time/residue: 0.2404 time to fit residues: 60.8095 Evaluate side-chains 159 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 0.0870 chunk 134 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 187 optimal weight: 0.3980 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 128 optimal weight: 0.0370 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 16567 Z= 0.162 Angle : 0.602 10.806 22514 Z= 0.292 Chirality : 0.044 0.506 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.335 55.688 2402 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.07 % Allowed : 14.26 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.29 (0.19), residues: 2031 helix: 0.41 (0.35), residues: 217 sheet: 0.20 (0.17), residues: 902 loop : -0.65 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1036 HIS 0.003 0.000 HIS A 753 PHE 0.040 0.001 PHE A1286 TYR 0.015 0.001 TYR B 491 ARG 0.002 0.000 ARG B 774 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.728 Fit side-chains revert: symmetry clash REVERT: A 735 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6673 (mm-30) REVERT: A 985 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8766 (mm) REVERT: A 1015 MET cc_start: 0.7293 (pmm) cc_final: 0.6305 (tmm) REVERT: A 1065 TRP cc_start: 0.5953 (m100) cc_final: 0.5309 (m100) REVERT: A 1142 TYR cc_start: 0.8934 (t80) cc_final: 0.8660 (t80) REVERT: A 1173 TRP cc_start: 0.6452 (m-90) cc_final: 0.6161 (m-90) REVERT: B 67 GLU cc_start: 0.6620 (tp30) cc_final: 0.6249 (tp30) REVERT: B 157 MET cc_start: 0.7972 (ppp) cc_final: 0.7563 (ppp) REVERT: B 501 MET cc_start: 0.8107 (ttp) cc_final: 0.7683 (ttm) REVERT: B 608 SER cc_start: 0.8879 (t) cc_final: 0.8506 (p) outliers start: 37 outliers final: 32 residues processed: 157 average time/residue: 0.2328 time to fit residues: 60.6354 Evaluate side-chains 156 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 4.9990 chunk 49 optimal weight: 0.0270 chunk 149 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 162 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1288 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.116058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.082718 restraints weight = 42591.678| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.91 r_work: 0.3310 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 16567 Z= 0.164 Angle : 0.605 13.114 22514 Z= 0.291 Chirality : 0.044 0.498 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.224 55.448 2402 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.90 % Allowed : 14.37 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.23 (0.19), residues: 2031 helix: 0.45 (0.35), residues: 217 sheet: 0.21 (0.17), residues: 908 loop : -0.58 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1036 HIS 0.003 0.000 HIS A 753 PHE 0.016 0.001 PHE B 887 TYR 0.016 0.001 TYR B 491 ARG 0.002 0.000 ARG B 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3648.07 seconds wall clock time: 67 minutes 53.90 seconds (4073.90 seconds total)