Starting phenix.real_space_refine on Sat Aug 23 06:18:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8v_19012/08_2025/8r8v_19012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8v_19012/08_2025/8r8v_19012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r8v_19012/08_2025/8r8v_19012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8v_19012/08_2025/8r8v_19012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r8v_19012/08_2025/8r8v_19012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8v_19012/08_2025/8r8v_19012.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 10 9.91 5 S 74 5.16 5 C 6498 2.51 5 N 1714 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10202 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4987 Classifications: {'peptide': 634} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 589} Chain breaks: 3 Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 108 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 108 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4987 Classifications: {'peptide': 634} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 589} Chain breaks: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.71, per 1000 atoms: 0.27 Number of scatterers: 10202 At special positions: 0 Unit cell: (143.45, 94.05, 75.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 10 19.99 S 74 16.00 O 1906 8.00 N 1714 7.00 C 6498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 258.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 26 sheets defined 22.8% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 173 through 180 removed outlier: 3.542A pdb=" N MET A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 removed outlier: 3.505A pdb=" N THR A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 195' Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 533 through 557 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'B' and resid 173 through 180 removed outlier: 3.542A pdb=" N MET B 180 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 removed outlier: 3.505A pdb=" N THR B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 195' Processing helix chain 'B' and resid 316 through 331 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 444 through 454 Processing helix chain 'B' and resid 471 through 474 Processing helix chain 'B' and resid 494 through 507 Processing helix chain 'B' and resid 526 through 532 Processing helix chain 'B' and resid 533 through 557 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 611 through 621 Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 657 through 661 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.130A pdb=" N THR A 5 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP A 28 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 25 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 76 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.604A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.604A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 213 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 226 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 3.642A pdb=" N ALA A 148 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 271 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN A 286 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE A 269 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER A 288 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 267 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 290 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 265 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU A 199 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 337 removed outlier: 8.439A pdb=" N THR A 335 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 308 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N CYS A 337 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA A 310 " --> pdb=" O CYS A 337 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 307 " --> pdb=" O ARG A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 359 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480 removed outlier: 8.329A pdb=" N ILE A 565 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 489 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE A 567 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A 491 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AB2, first strand: chain 'A' and resid 571 through 573 Processing sheet with id=AB3, first strand: chain 'A' and resid 590 through 592 Processing sheet with id=AB4, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 6.130A pdb=" N THR B 5 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP B 28 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 7 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 25 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL B 76 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 15 through 20 removed outlier: 6.604A pdb=" N THR B 15 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR B 111 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 17 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL B 113 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS B 19 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE B 115 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 15 through 20 removed outlier: 6.604A pdb=" N THR B 15 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR B 111 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 17 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL B 113 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS B 19 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE B 115 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 213 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 226 " --> pdb=" O GLN B 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 150 removed outlier: 3.643A pdb=" N ALA B 148 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 271 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN B 286 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 269 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER B 288 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 267 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 290 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 265 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 199 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 335 through 337 removed outlier: 8.439A pdb=" N THR B 335 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 308 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N CYS B 337 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA B 310 " --> pdb=" O CYS B 337 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 307 " --> pdb=" O ARG B 650 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 359 Processing sheet with id=AC2, first strand: chain 'B' and resid 411 through 412 Processing sheet with id=AC3, first strand: chain 'B' and resid 416 through 418 Processing sheet with id=AC4, first strand: chain 'B' and resid 476 through 480 removed outlier: 8.328A pdb=" N ILE B 565 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 489 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE B 567 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU B 491 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 513 through 514 Processing sheet with id=AC6, first strand: chain 'B' and resid 571 through 573 Processing sheet with id=AC7, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AC8, first strand: chain 'B' and resid 605 through 606 368 hydrogen bonds defined for protein. 930 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: 1.86 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3140 1.34 - 1.45: 1508 1.45 - 1.57: 5676 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10432 Sorted by residual: bond pdb=" N PHE A 583 " pdb=" CA PHE A 583 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.59e+01 bond pdb=" N PHE B 583 " pdb=" CA PHE B 583 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.59e+01 bond pdb=" N VAL B 416 " pdb=" CA VAL B 416 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N VAL A 416 " pdb=" CA VAL A 416 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N ILE A 567 " pdb=" CA ILE A 567 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.16e+01 ... (remaining 10427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 13367 1.49 - 2.98: 657 2.98 - 4.47: 120 4.47 - 5.96: 8 5.96 - 7.44: 4 Bond angle restraints: 14156 Sorted by residual: angle pdb=" CA PHE A 487 " pdb=" CB PHE A 487 " pdb=" CG PHE A 487 " ideal model delta sigma weight residual 113.80 117.77 -3.97 1.00e+00 1.00e+00 1.58e+01 angle pdb=" C PHE B 583 " pdb=" CA PHE B 583 " pdb=" CB PHE B 583 " ideal model delta sigma weight residual 109.22 115.21 -5.99 1.52e+00 4.33e-01 1.55e+01 angle pdb=" C PHE A 583 " pdb=" CA PHE A 583 " pdb=" CB PHE A 583 " ideal model delta sigma weight residual 109.22 115.19 -5.97 1.52e+00 4.33e-01 1.54e+01 angle pdb=" CA PHE B 487 " pdb=" CB PHE B 487 " pdb=" CG PHE B 487 " ideal model delta sigma weight residual 113.80 117.71 -3.91 1.00e+00 1.00e+00 1.53e+01 angle pdb=" CA GLU B 315 " pdb=" CB GLU B 315 " pdb=" CG GLU B 315 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.39e+01 ... (remaining 14151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5547 17.71 - 35.42: 583 35.42 - 53.13: 132 53.13 - 70.84: 40 70.84 - 88.55: 10 Dihedral angle restraints: 6312 sinusoidal: 2576 harmonic: 3736 Sorted by residual: dihedral pdb=" CA ASN B 506 " pdb=" C ASN B 506 " pdb=" N GLU B 507 " pdb=" CA GLU B 507 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASN A 506 " pdb=" C ASN A 506 " pdb=" N GLU A 507 " pdb=" CA GLU A 507 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE A 314 " pdb=" C PHE A 314 " pdb=" N GLU A 315 " pdb=" CA GLU A 315 " ideal model delta harmonic sigma weight residual -180.00 -162.37 -17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1200 0.053 - 0.107: 281 0.107 - 0.160: 81 0.160 - 0.213: 14 0.213 - 0.267: 4 Chirality restraints: 1580 Sorted by residual: chirality pdb=" CA ILE B 630 " pdb=" N ILE B 630 " pdb=" C ILE B 630 " pdb=" CB ILE B 630 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ILE A 630 " pdb=" N ILE A 630 " pdb=" C ILE A 630 " pdb=" CB ILE A 630 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ILE B 565 " pdb=" N ILE B 565 " pdb=" C ILE B 565 " pdb=" CB ILE B 565 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1577 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 650 " -0.283 9.50e-02 1.11e+02 1.27e-01 9.91e+00 pdb=" NE ARG A 650 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 650 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 650 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 650 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 650 " -0.283 9.50e-02 1.11e+02 1.27e-01 9.89e+00 pdb=" NE ARG B 650 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 650 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 650 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 650 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 123 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.57e+00 pdb=" NE ARG B 123 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 123 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 123 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 123 " -0.010 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1820 2.77 - 3.30: 9133 3.30 - 3.84: 16022 3.84 - 4.37: 18790 4.37 - 4.90: 32838 Nonbonded interactions: 78603 Sorted by model distance: nonbonded pdb=" OD1 ASP A 155 " pdb="CA CA A 901 " model vdw 2.238 2.510 nonbonded pdb=" OD1 ASP B 155 " pdb="CA CA B 901 " model vdw 2.238 2.510 nonbonded pdb=" OD1 ASP B 176 " pdb="CA CA B 901 " model vdw 2.258 2.510 nonbonded pdb=" OD1 ASP A 176 " pdb="CA CA A 901 " model vdw 2.258 2.510 nonbonded pdb=" OD2 ASP A 179 " pdb="CA CA A 902 " model vdw 2.263 2.510 ... (remaining 78598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.010 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.005 0.096 10434 Z= 0.347 Angle : 0.717 7.444 14156 Z= 0.456 Chirality : 0.054 0.267 1580 Planarity : 0.009 0.127 1832 Dihedral : 15.813 88.546 3888 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.61 % Allowed : 20.83 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.23), residues: 1272 helix: 0.84 (0.36), residues: 238 sheet: 0.30 (0.26), residues: 406 loop : -0.97 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 374 TYR 0.011 0.001 TYR C 6 PHE 0.023 0.002 PHE A 576 TRP 0.010 0.001 TRP A 347 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00483 (10432) covalent geometry : angle 0.71714 (14156) hydrogen bonds : bond 0.11452 ( 368) hydrogen bonds : angle 5.90691 ( 930) Misc. bond : bond 0.09536 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.420 Fit side-chains REVERT: A 8 ARG cc_start: 0.6922 (ptp90) cc_final: 0.6670 (ptt-90) REVERT: B 6 LEU cc_start: 0.8550 (tp) cc_final: 0.8299 (tt) REVERT: B 8 ARG cc_start: 0.7007 (ptp90) cc_final: 0.6633 (ptp-170) REVERT: B 24 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7467 (pt) outliers start: 7 outliers final: 0 residues processed: 187 average time/residue: 0.1238 time to fit residues: 31.3266 Evaluate side-chains 152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0040 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.152595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116061 restraints weight = 12415.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119200 restraints weight = 9194.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120030 restraints weight = 6747.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120420 restraints weight = 5954.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120709 restraints weight = 5117.714| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10434 Z= 0.124 Angle : 0.543 8.812 14156 Z= 0.284 Chirality : 0.044 0.154 1580 Planarity : 0.006 0.085 1832 Dihedral : 4.328 32.197 1370 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.60 % Allowed : 19.62 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.23), residues: 1272 helix: 1.45 (0.36), residues: 228 sheet: 0.56 (0.26), residues: 400 loop : -0.62 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 8 TYR 0.005 0.001 TYR A 356 PHE 0.019 0.001 PHE A 291 TRP 0.008 0.001 TRP B 347 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00288 (10432) covalent geometry : angle 0.54335 (14156) hydrogen bonds : bond 0.03918 ( 368) hydrogen bonds : angle 4.93808 ( 930) Misc. bond : bond 0.00008 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.434 Fit side-chains REVERT: A 183 MET cc_start: 0.7952 (ttm) cc_final: 0.7618 (ttm) REVERT: A 346 GLN cc_start: 0.8116 (pm20) cc_final: 0.7914 (pm20) REVERT: A 438 ASN cc_start: 0.8007 (p0) cc_final: 0.7615 (p0) REVERT: A 639 ARG cc_start: 0.7678 (mtt90) cc_final: 0.7402 (mtm-85) REVERT: B 123 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7787 (mtt-85) REVERT: B 183 MET cc_start: 0.7956 (ttm) cc_final: 0.7607 (ttm) REVERT: B 346 GLN cc_start: 0.8122 (pm20) cc_final: 0.7889 (pm20) REVERT: B 438 ASN cc_start: 0.8021 (p0) cc_final: 0.7639 (p0) outliers start: 30 outliers final: 8 residues processed: 182 average time/residue: 0.1090 time to fit residues: 27.7018 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 363 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 96 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.146695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.111039 restraints weight = 12677.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112598 restraints weight = 11297.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113953 restraints weight = 8100.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114398 restraints weight = 6401.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114685 restraints weight = 6092.448| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10434 Z= 0.224 Angle : 0.603 8.598 14156 Z= 0.312 Chirality : 0.047 0.196 1580 Planarity : 0.005 0.053 1832 Dihedral : 4.683 25.756 1368 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.60 % Allowed : 19.53 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.24), residues: 1272 helix: 1.38 (0.36), residues: 226 sheet: 0.53 (0.26), residues: 404 loop : -0.62 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 650 TYR 0.010 0.002 TYR B 237 PHE 0.021 0.002 PHE A 583 TRP 0.012 0.002 TRP B 141 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00551 (10432) covalent geometry : angle 0.60256 (14156) hydrogen bonds : bond 0.04403 ( 368) hydrogen bonds : angle 5.05003 ( 930) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7985 (mtt-85) REVERT: A 156 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.6481 (ptp-170) REVERT: A 438 ASN cc_start: 0.8322 (p0) cc_final: 0.7739 (p0) REVERT: A 449 ASP cc_start: 0.7738 (m-30) cc_final: 0.7218 (m-30) REVERT: A 495 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7731 (mtm110) REVERT: A 550 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7714 (ttt90) REVERT: A 551 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7317 (tm-30) REVERT: A 639 ARG cc_start: 0.7581 (mtt90) cc_final: 0.7097 (mtm-85) REVERT: B 123 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7907 (mtt-85) REVERT: B 156 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.6503 (ptp-170) REVERT: B 438 ASN cc_start: 0.8331 (p0) cc_final: 0.7746 (p0) REVERT: B 449 ASP cc_start: 0.7757 (m-30) cc_final: 0.7250 (m-30) REVERT: B 493 SER cc_start: 0.8698 (m) cc_final: 0.8479 (p) REVERT: B 550 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7651 (ttt90) REVERT: B 551 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7303 (tm-30) REVERT: B 639 ARG cc_start: 0.7616 (mtt90) cc_final: 0.7208 (mtm-85) outliers start: 53 outliers final: 25 residues processed: 190 average time/residue: 0.1274 time to fit residues: 32.9795 Evaluate side-chains 182 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 649 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 117 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 78 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.153142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115543 restraints weight = 12583.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119645 restraints weight = 8275.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120846 restraints weight = 5221.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121292 restraints weight = 4500.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121564 restraints weight = 4206.092| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10434 Z= 0.113 Angle : 0.527 8.554 14156 Z= 0.270 Chirality : 0.044 0.150 1580 Planarity : 0.005 0.049 1832 Dihedral : 4.269 23.441 1368 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.21 % Allowed : 20.92 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.24), residues: 1272 helix: 1.85 (0.37), residues: 212 sheet: 0.68 (0.26), residues: 402 loop : -0.51 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.005 0.001 TYR B 356 PHE 0.012 0.001 PHE A 407 TRP 0.010 0.001 TRP B 347 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00267 (10432) covalent geometry : angle 0.52721 (14156) hydrogen bonds : bond 0.03555 ( 368) hydrogen bonds : angle 4.72742 ( 930) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7724 (mtt-85) REVERT: A 156 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.6628 (ptp-170) REVERT: A 438 ASN cc_start: 0.8170 (p0) cc_final: 0.7496 (p0) REVERT: A 550 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7589 (ttt90) REVERT: A 551 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7298 (tm-30) REVERT: A 576 PHE cc_start: 0.7313 (m-80) cc_final: 0.6948 (m-80) REVERT: A 639 ARG cc_start: 0.7589 (mtt90) cc_final: 0.7093 (mtm-85) REVERT: B 123 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7766 (mtt-85) REVERT: B 156 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.6642 (ptp-170) REVERT: B 438 ASN cc_start: 0.8195 (p0) cc_final: 0.7527 (p0) REVERT: B 493 SER cc_start: 0.8684 (m) cc_final: 0.8429 (p) REVERT: B 495 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7606 (mtm110) REVERT: B 550 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7565 (ttt90) REVERT: B 551 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7317 (tm-30) REVERT: B 576 PHE cc_start: 0.7313 (m-80) cc_final: 0.6944 (m-80) REVERT: B 639 ARG cc_start: 0.7563 (mtt90) cc_final: 0.7103 (mtm-85) outliers start: 37 outliers final: 17 residues processed: 193 average time/residue: 0.1271 time to fit residues: 33.2098 Evaluate side-chains 176 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 550 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.114697 restraints weight = 12587.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115783 restraints weight = 7666.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.117233 restraints weight = 6263.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118028 restraints weight = 5089.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118684 restraints weight = 4594.001| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10434 Z= 0.136 Angle : 0.538 8.276 14156 Z= 0.275 Chirality : 0.044 0.171 1580 Planarity : 0.004 0.047 1832 Dihedral : 4.273 25.611 1368 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.17 % Allowed : 20.31 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.24), residues: 1272 helix: 1.94 (0.38), residues: 214 sheet: 0.76 (0.26), residues: 406 loop : -0.45 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.006 0.001 TYR D 6 PHE 0.015 0.002 PHE A 583 TRP 0.009 0.001 TRP B 347 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00331 (10432) covalent geometry : angle 0.53756 (14156) hydrogen bonds : bond 0.03660 ( 368) hydrogen bonds : angle 4.70275 ( 930) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7796 (mtt-85) REVERT: A 156 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.6581 (ptp-170) REVERT: A 318 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7902 (t70) REVERT: A 438 ASN cc_start: 0.8413 (p0) cc_final: 0.7784 (p0) REVERT: A 499 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7958 (ttpt) REVERT: A 503 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8143 (mt-10) REVERT: A 507 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8035 (mt-10) REVERT: A 550 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7589 (ttt90) REVERT: A 551 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7285 (tm-30) REVERT: A 639 ARG cc_start: 0.7659 (mtt90) cc_final: 0.7195 (mtm-85) REVERT: B 123 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7798 (mtt-85) REVERT: B 156 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.6585 (ptp-170) REVERT: B 438 ASN cc_start: 0.8436 (p0) cc_final: 0.7777 (p0) REVERT: B 493 SER cc_start: 0.8738 (m) cc_final: 0.8509 (p) REVERT: B 495 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7556 (mtm110) REVERT: B 509 HIS cc_start: 0.8243 (m90) cc_final: 0.7721 (m90) REVERT: B 547 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8384 (t0) REVERT: B 550 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7568 (ttt90) REVERT: B 551 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7318 (tm-30) REVERT: B 639 ARG cc_start: 0.7613 (mtt90) cc_final: 0.7176 (mtm-85) outliers start: 48 outliers final: 28 residues processed: 195 average time/residue: 0.1296 time to fit residues: 34.0828 Evaluate side-chains 203 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 649 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113508 restraints weight = 12757.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116586 restraints weight = 8536.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117957 restraints weight = 5644.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119225 restraints weight = 5063.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119486 restraints weight = 4759.997| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10434 Z= 0.160 Angle : 0.554 8.108 14156 Z= 0.283 Chirality : 0.045 0.179 1580 Planarity : 0.005 0.046 1832 Dihedral : 4.456 30.638 1368 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.69 % Allowed : 20.23 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.24), residues: 1272 helix: 1.88 (0.37), residues: 214 sheet: 0.67 (0.26), residues: 408 loop : -0.48 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 374 TYR 0.008 0.001 TYR B 391 PHE 0.016 0.002 PHE B 583 TRP 0.009 0.001 TRP B 141 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00392 (10432) covalent geometry : angle 0.55392 (14156) hydrogen bonds : bond 0.03778 ( 368) hydrogen bonds : angle 4.71242 ( 930) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7907 (mmt) cc_final: 0.7406 (mmt) REVERT: A 123 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7814 (mtt-85) REVERT: A 156 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.6556 (ptp-170) REVERT: A 314 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 318 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7942 (t70) REVERT: A 438 ASN cc_start: 0.8420 (p0) cc_final: 0.7814 (p0) REVERT: A 499 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7976 (ttpt) REVERT: A 503 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8163 (mt-10) REVERT: A 507 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7980 (mt-10) REVERT: A 550 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7625 (ttt90) REVERT: A 551 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7302 (tm-30) REVERT: B 80 MET cc_start: 0.7930 (mmt) cc_final: 0.7257 (mmt) REVERT: B 123 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7830 (mtt-85) REVERT: B 156 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.6535 (ptp-170) REVERT: B 314 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6803 (t80) REVERT: B 381 ILE cc_start: 0.8995 (tp) cc_final: 0.8777 (tp) REVERT: B 438 ASN cc_start: 0.8432 (p0) cc_final: 0.7830 (p0) REVERT: B 495 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7560 (mtm110) REVERT: B 503 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8271 (mt-10) REVERT: B 547 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8429 (t0) REVERT: B 550 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7580 (ttt90) REVERT: B 551 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7301 (tm-30) outliers start: 54 outliers final: 31 residues processed: 191 average time/residue: 0.1310 time to fit residues: 33.5758 Evaluate side-chains 195 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 649 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112790 restraints weight = 12617.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116477 restraints weight = 7475.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118899 restraints weight = 5449.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120365 restraints weight = 4492.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121447 restraints weight = 3997.895| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10434 Z= 0.138 Angle : 0.542 8.106 14156 Z= 0.277 Chirality : 0.045 0.168 1580 Planarity : 0.005 0.044 1832 Dihedral : 4.369 32.049 1368 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.08 % Allowed : 20.49 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.24), residues: 1272 helix: 1.98 (0.38), residues: 214 sheet: 0.82 (0.26), residues: 406 loop : -0.49 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 374 TYR 0.006 0.001 TYR B 391 PHE 0.022 0.002 PHE B 40 TRP 0.007 0.001 TRP B 141 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00335 (10432) covalent geometry : angle 0.54198 (14156) hydrogen bonds : bond 0.03593 ( 368) hydrogen bonds : angle 4.63742 ( 930) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7720 (ptp90) cc_final: 0.6560 (ptp90) REVERT: A 80 MET cc_start: 0.7936 (mmt) cc_final: 0.7417 (mmt) REVERT: A 123 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7770 (mtt-85) REVERT: A 156 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6700 (ptp-170) REVERT: A 318 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7949 (t70) REVERT: A 438 ASN cc_start: 0.8331 (p0) cc_final: 0.7688 (p0) REVERT: A 499 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7993 (ttpt) REVERT: A 503 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8166 (mt-10) REVERT: A 507 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7960 (mt-10) REVERT: A 550 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7630 (ttt90) REVERT: A 551 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7322 (tm-30) REVERT: B 80 MET cc_start: 0.7942 (mmt) cc_final: 0.7270 (mmt) REVERT: B 123 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7780 (mtt-85) REVERT: B 156 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6716 (ptp-170) REVERT: B 314 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6823 (t80) REVERT: B 438 ASN cc_start: 0.8323 (p0) cc_final: 0.7683 (p0) REVERT: B 495 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.6826 (mtm110) REVERT: B 503 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8289 (mt-10) REVERT: B 547 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8311 (t0) REVERT: B 550 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7615 (ttt90) REVERT: B 551 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7350 (tm-30) outliers start: 47 outliers final: 34 residues processed: 191 average time/residue: 0.1347 time to fit residues: 34.6526 Evaluate side-chains 199 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 649 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 chunk 49 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109961 restraints weight = 12703.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113583 restraints weight = 7622.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115924 restraints weight = 5596.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117239 restraints weight = 4644.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.118382 restraints weight = 4150.849| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10434 Z= 0.170 Angle : 0.566 7.984 14156 Z= 0.291 Chirality : 0.046 0.183 1580 Planarity : 0.005 0.045 1832 Dihedral : 4.577 36.960 1368 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.34 % Allowed : 20.40 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.24), residues: 1272 helix: 1.94 (0.38), residues: 214 sheet: 0.71 (0.26), residues: 408 loop : -0.50 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 374 TYR 0.009 0.001 TYR B 391 PHE 0.024 0.002 PHE A 40 TRP 0.009 0.001 TRP B 141 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00419 (10432) covalent geometry : angle 0.56621 (14156) hydrogen bonds : bond 0.03830 ( 368) hydrogen bonds : angle 4.72791 ( 930) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7951 (mmt) cc_final: 0.7414 (mmt) REVERT: A 123 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7839 (mtt-85) REVERT: A 156 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.6618 (ptp-170) REVERT: A 314 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6741 (t80) REVERT: A 318 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7965 (t70) REVERT: A 438 ASN cc_start: 0.8324 (p0) cc_final: 0.7697 (p0) REVERT: A 499 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7961 (ttpt) REVERT: A 503 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8148 (mt-10) REVERT: A 507 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8049 (mt-10) REVERT: A 509 HIS cc_start: 0.8068 (m90) cc_final: 0.7605 (m90) REVERT: A 550 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7629 (ttt90) REVERT: A 551 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7331 (tm-30) REVERT: B 80 MET cc_start: 0.7983 (mmt) cc_final: 0.7318 (mmt) REVERT: B 123 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7852 (mtt-85) REVERT: B 156 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6703 (ptp-170) REVERT: B 314 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6782 (t80) REVERT: B 438 ASN cc_start: 0.8272 (p0) cc_final: 0.7664 (p0) REVERT: B 495 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6929 (mtm110) REVERT: B 503 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8315 (mt-10) REVERT: B 547 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8356 (t0) REVERT: B 550 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7614 (ttt90) REVERT: B 551 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7331 (tm-30) outliers start: 50 outliers final: 33 residues processed: 194 average time/residue: 0.1352 time to fit residues: 35.4297 Evaluate side-chains 197 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 649 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 57 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115247 restraints weight = 12641.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118847 restraints weight = 7687.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121275 restraints weight = 5653.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122827 restraints weight = 4667.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123650 restraints weight = 4150.092| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10434 Z= 0.134 Angle : 0.553 8.018 14156 Z= 0.282 Chirality : 0.045 0.165 1580 Planarity : 0.005 0.051 1832 Dihedral : 4.435 35.515 1368 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.51 % Allowed : 20.40 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.24), residues: 1272 helix: 2.03 (0.38), residues: 214 sheet: 0.81 (0.26), residues: 408 loop : -0.43 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 495 TYR 0.008 0.001 TYR D 6 PHE 0.023 0.002 PHE A 40 TRP 0.007 0.001 TRP B 347 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00327 (10432) covalent geometry : angle 0.55349 (14156) hydrogen bonds : bond 0.03550 ( 368) hydrogen bonds : angle 4.63442 ( 930) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7929 (mmt) cc_final: 0.7519 (mmt) REVERT: A 123 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7753 (mtt-85) REVERT: A 156 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.6638 (ptp-170) REVERT: A 314 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6775 (t80) REVERT: A 318 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7961 (t70) REVERT: A 383 ARG cc_start: 0.7357 (tpp-160) cc_final: 0.6827 (ttm-80) REVERT: A 438 ASN cc_start: 0.8280 (p0) cc_final: 0.7640 (p0) REVERT: A 499 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7970 (ttpt) REVERT: A 503 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8135 (mt-10) REVERT: A 507 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8094 (mt-10) REVERT: A 509 HIS cc_start: 0.8066 (m90) cc_final: 0.7672 (m90) REVERT: A 550 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7492 (ttt90) REVERT: A 551 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7287 (tm-30) REVERT: B 80 MET cc_start: 0.7987 (mmt) cc_final: 0.7459 (mmt) REVERT: B 123 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7772 (mtt-85) REVERT: B 156 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.6638 (ptp-170) REVERT: B 314 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6298 (t80) REVERT: B 315 GLU cc_start: 0.7844 (mp0) cc_final: 0.7290 (mp0) REVERT: B 318 ASP cc_start: 0.8378 (p0) cc_final: 0.7963 (t70) REVERT: B 383 ARG cc_start: 0.7360 (tpp-160) cc_final: 0.6831 (ttm-80) REVERT: B 438 ASN cc_start: 0.8277 (p0) cc_final: 0.7646 (p0) REVERT: B 495 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7362 (mtm110) REVERT: B 509 HIS cc_start: 0.8138 (m90) cc_final: 0.7680 (m90) REVERT: B 547 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8343 (t0) REVERT: B 550 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7542 (ttt90) REVERT: B 551 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7297 (tm-30) outliers start: 52 outliers final: 34 residues processed: 192 average time/residue: 0.1293 time to fit residues: 33.6552 Evaluate side-chains 194 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.0030 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118632 restraints weight = 12396.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122359 restraints weight = 7425.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124825 restraints weight = 5427.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126477 restraints weight = 4460.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127470 restraints weight = 3943.649| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10434 Z= 0.117 Angle : 0.564 8.358 14156 Z= 0.284 Chirality : 0.044 0.157 1580 Planarity : 0.005 0.053 1832 Dihedral : 4.289 32.071 1368 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.21 % Allowed : 21.96 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.24), residues: 1272 helix: 2.10 (0.38), residues: 214 sheet: 0.91 (0.26), residues: 406 loop : -0.40 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 495 TYR 0.007 0.001 TYR D 6 PHE 0.023 0.001 PHE A 40 TRP 0.007 0.001 TRP A 659 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00279 (10432) covalent geometry : angle 0.56364 (14156) hydrogen bonds : bond 0.03390 ( 368) hydrogen bonds : angle 4.54178 ( 930) Misc. bond : bond 0.00007 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7951 (mmt) cc_final: 0.7674 (mmt) REVERT: A 123 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7519 (mtt-85) REVERT: A 156 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.6704 (ptp-170) REVERT: A 314 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6776 (t80) REVERT: A 318 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7985 (t70) REVERT: A 383 ARG cc_start: 0.7330 (tpp-160) cc_final: 0.6810 (ttm-80) REVERT: A 438 ASN cc_start: 0.8245 (p0) cc_final: 0.7623 (p0) REVERT: A 499 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7963 (ttpt) REVERT: A 503 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8099 (mt-10) REVERT: A 507 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8123 (mt-10) REVERT: A 509 HIS cc_start: 0.7983 (m90) cc_final: 0.7751 (m90) REVERT: A 550 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7549 (ttt90) REVERT: A 551 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7269 (tm-30) REVERT: B 80 MET cc_start: 0.7996 (mmt) cc_final: 0.7683 (mmt) REVERT: B 123 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7659 (mtt-85) REVERT: B 156 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.6684 (ptp-170) REVERT: B 314 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6307 (t80) REVERT: B 315 GLU cc_start: 0.7810 (mp0) cc_final: 0.7263 (mp0) REVERT: B 318 ASP cc_start: 0.8354 (p0) cc_final: 0.7964 (t70) REVERT: B 383 ARG cc_start: 0.7339 (tpp-160) cc_final: 0.6812 (ttm-80) REVERT: B 438 ASN cc_start: 0.8255 (p0) cc_final: 0.7636 (p0) REVERT: B 495 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7381 (mtm110) REVERT: B 503 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8289 (mt-10) REVERT: B 509 HIS cc_start: 0.8065 (m90) cc_final: 0.7817 (m90) REVERT: B 550 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7450 (ttt90) REVERT: B 551 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7304 (tm-30) outliers start: 37 outliers final: 24 residues processed: 181 average time/residue: 0.1198 time to fit residues: 29.8364 Evaluate side-chains 181 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 550 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 chunk 122 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.158219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119267 restraints weight = 12536.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122896 restraints weight = 7599.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125331 restraints weight = 5573.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126899 restraints weight = 4606.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127769 restraints weight = 4091.136| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10434 Z= 0.117 Angle : 0.558 7.908 14156 Z= 0.281 Chirality : 0.044 0.154 1580 Planarity : 0.005 0.053 1832 Dihedral : 4.198 29.023 1368 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.04 % Allowed : 22.14 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.24), residues: 1272 helix: 2.19 (0.38), residues: 214 sheet: 0.98 (0.26), residues: 406 loop : -0.37 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 374 TYR 0.006 0.001 TYR D 6 PHE 0.023 0.001 PHE A 40 TRP 0.006 0.001 TRP B 347 HIS 0.003 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00281 (10432) covalent geometry : angle 0.55755 (14156) hydrogen bonds : bond 0.03339 ( 368) hydrogen bonds : angle 4.46557 ( 930) Misc. bond : bond 0.00009 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.41 seconds wall clock time: 32 minutes 52.30 seconds (1972.30 seconds total)