Starting phenix.real_space_refine on Thu Jul 2 20:46:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8v_19012/07_2026/8r8v_19012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8v_19012/07_2026/8r8v_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_19012/07_2026/8r8v_19012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8v_19012/07_2026/8r8v_19012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r8v_19012/07_2026/8r8v_19012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8v_19012/07_2026/8r8v_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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 5} Chain breaks: 5 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 0 Ad-hoc single atom residues: {' CA': 5} Chain breaks: 5 Time building chain proxies: 1.75, per 1000 atoms: 0.17 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: 0.88 Conformation dependent library (CDL) restraints added in 270.0 milliseconds 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: 0.21 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: 1.15 Time building geometry restraints manager: 1.08 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 3.250 nonbonded pdb=" OD1 ASP B 155 " pdb="CA CA B 901 " model vdw 2.238 3.250 nonbonded pdb=" OD1 ASP B 176 " pdb="CA CA B 901 " model vdw 2.258 3.250 nonbonded pdb=" OD1 ASP A 176 " pdb="CA CA A 901 " model vdw 2.258 3.250 nonbonded pdb=" OD2 ASP A 179 " pdb="CA CA A 902 " model vdw 2.263 3.250 ... (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: 0.01 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.900 Find NCS groups from input model: 0.060 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 are 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/Z covalent geometry : bond 0.00483 / 0.32 (10432) covalent geometry : angle 0.71714 / 0.46 (14156) hydrogen bonds : bond 0.11452 / 8.14 ( 368) hydrogen bonds : angle 5.90691 / 4.02 ( 930) Misc. bond : bond 0.09536 / 5.64 ( 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 : 0.250 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: 0.1023 time to fit residues: 26.0576 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 : 0.361 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0040 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3679 r_free = 0.3679 target = 0.152836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116345 restraints weight = 12381.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118347 restraints weight = 10071.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119711 restraints weight = 7484.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120735 restraints weight = 5845.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121128 restraints weight = 5331.914| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1260 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= 0.123 Angle : 0.542 8.700 14156 Z= 0.284 Chirality : 0.045 0.157 1580 Planarity : 0.005 0.083 1832 Dihedral : 4.358 32.539 1370 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.12 % Allowed : 18.75 % Favored : 78.12 % 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 are not related in a simple way. whole: 0.15 (0.23), residues: 1272 helix: 1.44 (0.36), residues: 228 sheet: 0.53 (0.26), residues: 402 loop : -0.65 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 8 TYR 0.006 0.001 TYR A 356 PHE 0.016 0.002 PHE A 291 TRP 0.008 0.001 TRP B 347 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (10432) covalent geometry : angle 0.54185 / 0.28 (14156) hydrogen bonds : bond 0.03842 / 2.74 ( 368) hydrogen bonds : angle 4.89965 / 3.38 ( 930) Misc. bond : bond 0.00009 / 0.01 ( 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 202 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.248 Fit side-chains REVERT: A 156 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.6624 (ptp-170) REVERT: A 346 GLN cc_start: 0.8116 (pm20) cc_final: 0.7914 (pm20) REVERT: A 438 ASN cc_start: 0.8015 (p0) cc_final: 0.7605 (p0) REVERT: A 449 ASP cc_start: 0.7590 (m-30) cc_final: 0.7241 (m-30) REVERT: A 639 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7353 (mtm-85) REVERT: B 156 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.6638 (ptp-170) REVERT: B 346 GLN cc_start: 0.8112 (pm20) cc_final: 0.7910 (pm20) REVERT: B 438 ASN cc_start: 0.8027 (p0) cc_final: 0.7624 (p0) REVERT: B 639 ARG cc_start: 0.7647 (mtt90) cc_final: 0.7361 (mtm-85) outliers start: 36 outliers final: 10 residues processed: 190 average time/residue: 0.0822 time to fit residues: 22.0673 Evaluate side-chains 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 389 PHE 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 156 ARG Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 389 PHE 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: 0.2980 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 0.1980 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.149845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112142 restraints weight = 12420.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114948 restraints weight = 8925.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115228 restraints weight = 6973.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115675 restraints weight = 6110.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116397 restraints weight = 5460.068| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1503 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= 0.142 Angle : 0.534 8.317 14156 Z= 0.276 Chirality : 0.045 0.158 1580 Planarity : 0.005 0.050 1832 Dihedral : 4.241 19.274 1368 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.91 % Allowed : 19.79 % Favored : 76.30 % 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 are not related in a simple way. whole: 0.32 (0.23), residues: 1272 helix: 1.45 (0.36), residues: 228 sheet: 0.68 (0.26), residues: 402 loop : -0.52 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 495 TYR 0.007 0.001 TYR B 391 PHE 0.017 0.002 PHE B 291 TRP 0.008 0.001 TRP A 347 HIS 0.003 0.001 HIS A 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (10432) covalent geometry : angle 0.53446 / 0.28 (14156) hydrogen bonds : bond 0.03772 / 2.67 ( 368) hydrogen bonds : angle 4.80028 / 3.33 ( 930) Misc. bond : bond 0.00014 / 0.01 ( 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 217 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7704 (mtt-85) REVERT: A 156 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6436 (ptp-170) REVERT: A 438 ASN cc_start: 0.8288 (p0) cc_final: 0.7700 (p0) REVERT: A 449 ASP cc_start: 0.7700 (m-30) cc_final: 0.7202 (m-30) REVERT: A 495 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7606 (mtm110) REVERT: A 509 HIS cc_start: 0.8129 (m90) cc_final: 0.7820 (m90) REVERT: A 550 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7474 (ttt90) REVERT: A 551 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7248 (tm-30) REVERT: A 639 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7174 (mtm-85) REVERT: B 123 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7694 (mtt-85) REVERT: B 156 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6508 (ptp-170) REVERT: B 438 ASN cc_start: 0.8291 (p0) cc_final: 0.7703 (p0) REVERT: B 449 ASP cc_start: 0.7719 (m-30) cc_final: 0.7253 (m-30) REVERT: B 509 HIS cc_start: 0.8159 (m90) cc_final: 0.7831 (m90) REVERT: B 550 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7437 (ttt90) REVERT: B 551 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7238 (tm-30) REVERT: B 639 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7173 (mtm-85) outliers start: 45 outliers final: 20 residues processed: 202 average time/residue: 0.0916 time to fit residues: 25.7597 Evaluate side-chains 188 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 239 MET Chi-restraints excluded: chain A residue 313 ILE 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 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 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 313 ILE 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 649 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 79 optimal weight: 0.0370 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110509 restraints weight = 12725.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.113701 restraints weight = 9054.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.115336 restraints weight = 6052.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.115396 restraints weight = 5075.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115781 restraints weight = 4800.639| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10434 Z= 0.194 Angle : 0.587 8.393 14156 Z= 0.302 Chirality : 0.046 0.190 1580 Planarity : 0.005 0.051 1832 Dihedral : 4.573 26.283 1368 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.08 % Allowed : 21.01 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1272 helix: 1.49 (0.37), residues: 226 sheet: 0.60 (0.27), residues: 400 loop : -0.63 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.010 0.002 TYR B 391 PHE 0.020 0.002 PHE A 583 TRP 0.010 0.001 TRP B 141 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.19 (10432) covalent geometry : angle 0.58654 / 0.30 (14156) hydrogen bonds : bond 0.04124 / 2.92 ( 368) hydrogen bonds : angle 4.87028 / 3.40 ( 930) Misc. bond : bond 0.00029 / 0.02 ( 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 200 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7864 (mp) cc_final: 0.7591 (pt) REVERT: A 123 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7912 (mtt-85) REVERT: A 156 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.6484 (ptp-170) REVERT: A 438 ASN cc_start: 0.8465 (p0) cc_final: 0.7832 (p0) REVERT: A 449 ASP cc_start: 0.7766 (m-30) cc_final: 0.7486 (m-30) REVERT: A 550 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7654 (ttt90) REVERT: A 551 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7275 (tm-30) REVERT: A 576 PHE cc_start: 0.7325 (m-80) cc_final: 0.6913 (m-80) REVERT: A 639 ARG cc_start: 0.7599 (mtt90) cc_final: 0.7073 (mtm-85) REVERT: B 123 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7909 (mtt-85) REVERT: B 156 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.6503 (ptp-170) REVERT: B 438 ASN cc_start: 0.8447 (p0) cc_final: 0.7814 (p0) REVERT: B 449 ASP cc_start: 0.7774 (m-30) cc_final: 0.7509 (m-30) REVERT: B 493 SER cc_start: 0.8751 (m) cc_final: 0.8550 (p) REVERT: B 495 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7562 (mtm110) REVERT: B 547 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8374 (t0) REVERT: B 550 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7668 (ttt90) REVERT: B 551 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7289 (tm-30) REVERT: B 576 PHE cc_start: 0.7329 (m-80) cc_final: 0.6919 (m-80) REVERT: B 639 ARG cc_start: 0.7604 (mtt90) cc_final: 0.7081 (mtm-85) outliers start: 47 outliers final: 21 residues processed: 184 average time/residue: 0.0980 time to fit residues: 24.3976 Evaluate side-chains 178 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 ILE 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 638 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 50 VAL 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 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 547 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.150878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110923 restraints weight = 12569.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114528 restraints weight = 7501.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116901 restraints weight = 5492.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118450 restraints weight = 4538.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119271 restraints weight = 4020.033| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1913 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= 0.136 Angle : 0.540 8.398 14156 Z= 0.276 Chirality : 0.045 0.160 1580 Planarity : 0.005 0.048 1832 Dihedral : 4.395 27.589 1368 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.34 % Allowed : 19.62 % Favored : 76.04 % 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 are not related in a simple way. whole: 0.32 (0.24), residues: 1272 helix: 1.59 (0.37), residues: 224 sheet: 0.65 (0.26), residues: 406 loop : -0.54 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 374 TYR 0.007 0.001 TYR B 391 PHE 0.013 0.002 PHE B 583 TRP 0.008 0.001 TRP A 347 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10432) covalent geometry : angle 0.54032 / 0.28 (14156) hydrogen bonds : bond 0.03620 / 2.57 ( 368) hydrogen bonds : angle 4.73273 / 3.30 ( 930) Misc. bond : bond 0.00017 / 0.01 ( 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 207 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7787 (mp) cc_final: 0.7568 (pt) REVERT: A 123 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7822 (mtt-85) REVERT: A 156 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.6499 (ptp-170) REVERT: A 438 ASN cc_start: 0.8379 (p0) cc_final: 0.7733 (p0) REVERT: A 550 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7586 (ttt90) REVERT: A 551 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7300 (tm-30) REVERT: B 123 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7832 (mtt-85) REVERT: B 156 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.6523 (ptp-170) REVERT: B 318 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7920 (t70) REVERT: B 438 ASN cc_start: 0.8383 (p0) cc_final: 0.7744 (p0) REVERT: B 495 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7549 (mtm110) REVERT: B 499 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8048 (ttpt) REVERT: B 503 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8326 (mt-10) REVERT: B 547 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8388 (t0) REVERT: B 550 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7559 (ttt90) REVERT: B 551 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7307 (tm-30) outliers start: 50 outliers final: 24 residues processed: 192 average time/residue: 0.0988 time to fit residues: 25.6930 Evaluate side-chains 186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL 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 313 ILE 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 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 638 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 239 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 318 ASP 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 499 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 638 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 GLN B 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.146433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109047 restraints weight = 12955.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112317 restraints weight = 9210.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113258 restraints weight = 6024.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113686 restraints weight = 5151.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114090 restraints weight = 4868.572| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10434 Z= 0.219 Angle : 0.603 8.202 14156 Z= 0.311 Chirality : 0.047 0.202 1580 Planarity : 0.005 0.048 1832 Dihedral : 4.856 39.378 1368 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.60 % Allowed : 19.88 % 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 are not related in a simple way. whole: 0.07 (0.23), residues: 1272 helix: 1.44 (0.37), residues: 224 sheet: 0.55 (0.26), residues: 400 loop : -0.76 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 374 TYR 0.011 0.002 TYR A 391 PHE 0.023 0.002 PHE B 40 TRP 0.011 0.002 TRP B 141 HIS 0.005 0.001 HIS A 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.22 (10432) covalent geometry : angle 0.60327 / 0.31 (14156) hydrogen bonds : bond 0.04216 / 2.99 ( 368) hydrogen bonds : angle 4.91857 / 3.43 ( 930) Misc. bond : bond 0.00030 / 0.02 ( 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: 53 poor density : 154 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7761 (mm110) REVERT: A 123 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7990 (mtt-85) REVERT: A 156 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.6553 (ptp-170) REVERT: A 314 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6707 (t80) REVERT: A 438 ASN cc_start: 0.8553 (p0) cc_final: 0.7899 (p0) REVERT: A 449 ASP cc_start: 0.7794 (m-30) cc_final: 0.7454 (m-30) REVERT: A 503 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8066 (mt-10) REVERT: A 507 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8117 (mt-10) REVERT: A 550 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7736 (ttt90) REVERT: A 551 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7326 (tm-30) REVERT: B 123 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7978 (mtt-85) REVERT: B 156 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.6561 (ptp-170) REVERT: B 314 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6710 (t80) REVERT: B 318 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8021 (t70) REVERT: B 438 ASN cc_start: 0.8544 (p0) cc_final: 0.7895 (p0) REVERT: B 449 ASP cc_start: 0.7891 (m-30) cc_final: 0.7567 (m-30) REVERT: B 495 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7526 (mtm110) REVERT: B 499 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8035 (ttpt) REVERT: B 503 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8315 (mt-10) REVERT: B 547 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8415 (t0) REVERT: B 550 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7725 (ttt90) REVERT: B 551 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7340 (tm-30) outliers start: 53 outliers final: 33 residues processed: 194 average time/residue: 0.1008 time to fit residues: 26.6828 Evaluate side-chains 196 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE 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 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 284 VAL Chi-restraints excluded: chain A residue 314 PHE 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 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 42 ILE 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 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 318 ASP 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 499 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 547 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 91 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 0.0000 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3678 r_free = 0.3678 target = 0.152378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112454 restraints weight = 12622.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116135 restraints weight = 7500.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118584 restraints weight = 5476.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120159 restraints weight = 4508.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121012 restraints weight = 4003.982| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10434 Z= 0.116 Angle : 0.536 8.270 14156 Z= 0.272 Chirality : 0.044 0.162 1580 Planarity : 0.005 0.045 1832 Dihedral : 4.458 36.374 1368 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.73 % Allowed : 20.66 % Favored : 75.61 % 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 are not related in a simple way. whole: 0.47 (0.24), residues: 1272 helix: 1.97 (0.38), residues: 214 sheet: 0.70 (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 B 374 TYR 0.005 0.001 TYR A 391 PHE 0.022 0.001 PHE A 40 TRP 0.008 0.001 TRP A 659 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10432) covalent geometry : angle 0.53578 / 0.27 (14156) hydrogen bonds : bond 0.03479 / 2.47 ( 368) hydrogen bonds : angle 4.66095 / 3.26 ( 930) Misc. bond : bond 0.00010 / 0.01 ( 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 198 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7703 (ptp90) cc_final: 0.6514 (ptp90) REVERT: A 123 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7804 (mtt-85) REVERT: A 314 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6763 (t80) REVERT: A 318 ASP cc_start: 0.8345 (p0) cc_final: 0.7931 (t70) REVERT: A 438 ASN cc_start: 0.8331 (p0) cc_final: 0.7689 (p0) REVERT: A 507 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8063 (mt-10) REVERT: A 550 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7593 (ttt90) REVERT: A 551 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7293 (tm-30) REVERT: B 123 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7786 (mtt-85) REVERT: B 314 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6763 (t80) REVERT: B 318 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7958 (t70) REVERT: B 438 ASN cc_start: 0.8320 (p0) cc_final: 0.7694 (p0) REVERT: B 495 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6884 (mtm110) REVERT: B 499 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7997 (ttpt) REVERT: B 503 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8287 (mt-10) REVERT: B 547 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8375 (t0) REVERT: B 550 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7578 (ttt90) REVERT: B 551 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7327 (tm-30) outliers start: 43 outliers final: 28 residues processed: 185 average time/residue: 0.0945 time to fit residues: 24.1556 Evaluate side-chains 186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 259 THR 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 363 THR Chi-restraints excluded: chain A residue 388 ASP 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 B residue 7 ILE 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 189 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 259 THR 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 318 ASP Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 388 ASP 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 499 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 10 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.152215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112280 restraints weight = 12643.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115993 restraints weight = 7526.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118437 restraints weight = 5494.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119913 restraints weight = 4523.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120876 restraints weight = 4019.500| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10434 Z= 0.134 Angle : 0.552 8.018 14156 Z= 0.280 Chirality : 0.044 0.166 1580 Planarity : 0.005 0.050 1832 Dihedral : 4.433 36.745 1368 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.08 % Allowed : 20.57 % Favored : 75.35 % 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 are not related in a simple way. whole: 0.54 (0.24), residues: 1272 helix: 2.01 (0.38), residues: 214 sheet: 0.77 (0.26), residues: 406 loop : -0.44 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 374 TYR 0.007 0.001 TYR B 391 PHE 0.022 0.002 PHE B 40 TRP 0.008 0.001 TRP B 347 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (10432) covalent geometry : angle 0.55185 / 0.28 (14156) hydrogen bonds : bond 0.03524 / 2.51 ( 368) hydrogen bonds : angle 4.61190 / 3.23 ( 930) Misc. bond : bond 0.00013 / 0.01 ( 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 199 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7682 (ptp90) cc_final: 0.6476 (ptp90) REVERT: A 123 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7692 (mtt-85) REVERT: A 156 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.6580 (ptp-170) REVERT: A 314 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6762 (t80) REVERT: A 318 ASP cc_start: 0.8357 (p0) cc_final: 0.7942 (t70) REVERT: A 383 ARG cc_start: 0.7354 (tpp-160) cc_final: 0.6848 (ttm-80) REVERT: A 438 ASN cc_start: 0.8303 (p0) cc_final: 0.7667 (p0) REVERT: A 509 HIS cc_start: 0.8095 (m90) cc_final: 0.7643 (m90) REVERT: A 550 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7594 (ttt90) REVERT: A 551 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7318 (tm-30) REVERT: B 123 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7776 (mtt-85) REVERT: B 156 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.6523 (ptp-170) REVERT: B 314 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6785 (t80) REVERT: B 318 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7971 (t70) REVERT: B 383 ARG cc_start: 0.7365 (tpp-160) cc_final: 0.6848 (ttm-80) REVERT: B 438 ASN cc_start: 0.8297 (p0) cc_final: 0.7675 (p0) REVERT: B 495 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6797 (mtm110) REVERT: B 499 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8059 (ttpt) REVERT: B 503 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8012 (mt-10) REVERT: B 507 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8088 (mt-10) REVERT: B 547 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8396 (t0) REVERT: B 550 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7600 (ttt90) REVERT: B 551 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7341 (tm-30) outliers start: 47 outliers final: 31 residues processed: 186 average time/residue: 0.0952 time to fit residues: 24.2570 Evaluate side-chains 187 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 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 284 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ASP 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 C residue 3 SER 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 284 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 388 ASP 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 499 LYS Chi-restraints excluded: chain B residue 543 GLU 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: 2.9990 chunk 56 optimal weight: 0.0050 chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 0.0030 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.157591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117968 restraints weight = 12530.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121687 restraints weight = 7367.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124202 restraints weight = 5349.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125700 restraints weight = 4395.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126822 restraints weight = 3905.291| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10434 Z= 0.104 Angle : 0.538 8.046 14156 Z= 0.270 Chirality : 0.043 0.144 1580 Planarity : 0.005 0.052 1832 Dihedral : 4.160 29.811 1368 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.73 % Allowed : 20.83 % 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 are not related in a simple way. whole: 0.69 (0.24), residues: 1272 helix: 2.10 (0.38), residues: 214 sheet: 0.87 (0.26), residues: 406 loop : -0.34 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 495 TYR 0.004 0.001 TYR B 356 PHE 0.022 0.001 PHE A 40 TRP 0.009 0.001 TRP A 659 HIS 0.003 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (10432) covalent geometry : angle 0.53779 / 0.27 (14156) hydrogen bonds : bond 0.03209 / 2.27 ( 368) hydrogen bonds : angle 4.42159 / 3.11 ( 930) Misc. bond : bond 0.00005 / 0.00 ( 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 203 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7636 (ptp90) cc_final: 0.6360 (ptp90) REVERT: A 123 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7637 (mtt-85) REVERT: A 156 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.6643 (ptp-170) REVERT: A 314 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6322 (t80) REVERT: A 315 GLU cc_start: 0.7722 (mp0) cc_final: 0.7214 (mp0) REVERT: A 318 ASP cc_start: 0.8271 (p0) cc_final: 0.7884 (t70) REVERT: A 383 ARG cc_start: 0.7377 (tpp-160) cc_final: 0.6899 (ttm-80) REVERT: A 438 ASN cc_start: 0.8184 (p0) cc_final: 0.7560 (p0) REVERT: A 550 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7587 (ttt90) REVERT: A 551 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7328 (tm-30) REVERT: B 80 MET cc_start: 0.7829 (mmt) cc_final: 0.7498 (mmt) REVERT: B 123 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7571 (mtt-85) REVERT: B 156 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.6665 (ptp-170) REVERT: B 314 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6330 (t80) REVERT: B 315 GLU cc_start: 0.7752 (mp0) cc_final: 0.7216 (mp0) REVERT: B 318 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7988 (t70) REVERT: B 383 ARG cc_start: 0.7390 (tpp-160) cc_final: 0.7165 (tpp80) REVERT: B 438 ASN cc_start: 0.8181 (p0) cc_final: 0.7568 (p0) REVERT: B 495 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6682 (mtm110) REVERT: B 499 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8037 (ttpt) REVERT: B 503 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8018 (mt-10) REVERT: B 547 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8335 (t0) REVERT: B 550 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7589 (ttt90) REVERT: B 551 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7368 (tm-30) outliers start: 43 outliers final: 24 residues processed: 190 average time/residue: 0.0930 time to fit residues: 24.2180 Evaluate side-chains 181 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 239 MET 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 363 THR Chi-restraints excluded: chain A residue 388 ASP 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 A residue 649 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 284 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 388 ASP 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 499 LYS 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: 0.9990 chunk 19 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 45 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.0070 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120612 restraints weight = 12399.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124312 restraints weight = 7416.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126778 restraints weight = 5419.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128396 restraints weight = 4464.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129247 restraints weight = 3951.855| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10434 Z= 0.116 Angle : 0.571 8.933 14156 Z= 0.283 Chirality : 0.044 0.158 1580 Planarity : 0.005 0.051 1832 Dihedral : 4.167 26.805 1368 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.95 % Allowed : 23.18 % Favored : 73.87 % 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 are not related in a simple way. whole: 0.61 (0.24), residues: 1272 helix: 1.78 (0.37), residues: 226 sheet: 0.95 (0.26), residues: 402 loop : -0.43 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 495 TYR 0.005 0.001 TYR B 391 PHE 0.023 0.001 PHE A 40 TRP 0.006 0.001 TRP A 659 HIS 0.003 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10432) covalent geometry : angle 0.57113 / 0.28 (14156) hydrogen bonds : bond 0.03309 / 2.34 ( 368) hydrogen bonds : angle 4.41876 / 3.11 ( 930) Misc. bond : bond 0.00008 / 0.00 ( 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: 34 poor density : 156 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7628 (ptp90) cc_final: 0.6335 (ptp90) REVERT: A 123 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7621 (mtt-85) REVERT: A 156 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6518 (ptp-170) REVERT: A 314 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6216 (t80) REVERT: A 315 GLU cc_start: 0.7805 (mp0) cc_final: 0.7271 (mp0) REVERT: A 318 ASP cc_start: 0.8311 (p0) cc_final: 0.7875 (t70) REVERT: A 383 ARG cc_start: 0.7328 (tpp-160) cc_final: 0.6863 (ttm-80) REVERT: A 438 ASN cc_start: 0.8231 (p0) cc_final: 0.7587 (p0) REVERT: A 550 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7555 (ttt90) REVERT: A 551 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7274 (tm-30) REVERT: B 80 MET cc_start: 0.7910 (mmt) cc_final: 0.7578 (mmt) REVERT: B 123 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7597 (mtt-85) REVERT: B 156 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.6505 (ptp-170) REVERT: B 314 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6223 (t80) REVERT: B 315 GLU cc_start: 0.7822 (mp0) cc_final: 0.7264 (mp0) REVERT: B 318 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7998 (t70) REVERT: B 383 ARG cc_start: 0.7348 (tpp-160) cc_final: 0.7121 (tpp80) REVERT: B 438 ASN cc_start: 0.8268 (p0) cc_final: 0.7636 (p0) REVERT: B 495 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6744 (mtm110) REVERT: B 547 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8367 (t0) REVERT: B 550 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7570 (ttt90) REVERT: B 551 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7297 (tm-30) outliers start: 34 outliers final: 21 residues processed: 179 average time/residue: 0.0904 time to fit residues: 22.6191 Evaluate side-chains 183 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 313 ILE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ASP 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 A residue 649 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 239 MET 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 318 ASP Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 388 ASP 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 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116345 restraints weight = 12628.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120051 restraints weight = 7458.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.122533 restraints weight = 5423.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124002 restraints weight = 4449.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125089 restraints weight = 3952.403| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10434 Z= 0.129 Angle : 0.573 8.618 14156 Z= 0.285 Chirality : 0.044 0.166 1580 Planarity : 0.005 0.052 1832 Dihedral : 4.230 26.398 1368 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.56 % Allowed : 22.66 % Favored : 73.78 % 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 are not related in a simple way. whole: 0.56 (0.24), residues: 1272 helix: 1.74 (0.37), residues: 224 sheet: 0.94 (0.26), residues: 402 loop : -0.47 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 374 TYR 0.007 0.001 TYR B 391 PHE 0.023 0.002 PHE A 40 TRP 0.007 0.001 TRP B 141 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (10432) covalent geometry : angle 0.57262 / 0.28 (14156) hydrogen bonds : bond 0.03413 / 2.41 ( 368) hydrogen bonds : angle 4.43439 / 3.12 ( 930) Misc. bond : bond 0.00023 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1412.46 seconds wall clock time: 25 minutes 9.32 seconds (1509.32 seconds total)