Starting phenix.real_space_refine on Fri Jan 17 02:07:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8v_19012/01_2025/8r8v_19012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8v_19012/01_2025/8r8v_19012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r8v_19012/01_2025/8r8v_19012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8v_19012/01_2025/8r8v_19012.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8v_19012/01_2025/8r8v_19012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8v_19012/01_2025/8r8v_19012.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10202 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4987 Classifications: {'peptide': 634} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 589} Chain breaks: 3 Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 108 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 108 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4987 Classifications: {'peptide': 634} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 589} Chain breaks: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.19, per 1000 atoms: 0.61 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: 2.98 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.48 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: 3.41 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3140 1.34 - 1.45: 1508 1.45 - 1.57: 5676 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10432 Sorted by residual: bond pdb=" N PHE A 583 " pdb=" CA PHE A 583 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.59e+01 bond pdb=" N PHE B 583 " pdb=" CA PHE B 583 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.59e+01 bond pdb=" N VAL B 416 " pdb=" CA VAL B 416 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N VAL A 416 " pdb=" CA VAL A 416 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N ILE A 567 " pdb=" CA ILE A 567 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.16e+01 ... (remaining 10427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 13367 1.49 - 2.98: 657 2.98 - 4.47: 120 4.47 - 5.96: 8 5.96 - 7.44: 4 Bond angle restraints: 14156 Sorted by residual: angle pdb=" CA PHE A 487 " pdb=" CB PHE A 487 " pdb=" CG PHE A 487 " ideal model delta sigma weight residual 113.80 117.77 -3.97 1.00e+00 1.00e+00 1.58e+01 angle pdb=" C PHE B 583 " pdb=" CA PHE B 583 " pdb=" CB PHE B 583 " ideal model delta sigma weight residual 109.22 115.21 -5.99 1.52e+00 4.33e-01 1.55e+01 angle pdb=" C PHE A 583 " pdb=" CA PHE A 583 " pdb=" CB PHE A 583 " ideal model delta sigma weight residual 109.22 115.19 -5.97 1.52e+00 4.33e-01 1.54e+01 angle pdb=" CA PHE B 487 " pdb=" CB PHE B 487 " pdb=" CG PHE B 487 " ideal model delta sigma weight residual 113.80 117.71 -3.91 1.00e+00 1.00e+00 1.53e+01 angle pdb=" CA GLU B 315 " pdb=" CB GLU B 315 " pdb=" CG GLU B 315 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.39e+01 ... (remaining 14151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5547 17.71 - 35.42: 583 35.42 - 53.13: 132 53.13 - 70.84: 40 70.84 - 88.55: 10 Dihedral angle restraints: 6312 sinusoidal: 2576 harmonic: 3736 Sorted by residual: dihedral pdb=" CA ASN B 506 " pdb=" C ASN B 506 " pdb=" N GLU B 507 " pdb=" CA GLU B 507 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASN A 506 " pdb=" C ASN A 506 " pdb=" N GLU A 507 " pdb=" CA GLU A 507 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE A 314 " pdb=" C PHE A 314 " pdb=" N GLU A 315 " pdb=" CA GLU A 315 " ideal model delta harmonic sigma weight residual -180.00 -162.37 -17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1200 0.053 - 0.107: 281 0.107 - 0.160: 81 0.160 - 0.213: 14 0.213 - 0.267: 4 Chirality restraints: 1580 Sorted by residual: chirality pdb=" CA ILE B 630 " pdb=" N ILE B 630 " pdb=" C ILE B 630 " pdb=" CB ILE B 630 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ILE A 630 " pdb=" N ILE A 630 " pdb=" C ILE A 630 " pdb=" CB ILE A 630 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ILE B 565 " pdb=" N ILE B 565 " pdb=" C ILE B 565 " pdb=" CB ILE B 565 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1577 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 650 " -0.283 9.50e-02 1.11e+02 1.27e-01 9.91e+00 pdb=" NE ARG A 650 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 650 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 650 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 650 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 650 " -0.283 9.50e-02 1.11e+02 1.27e-01 9.89e+00 pdb=" NE ARG B 650 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 650 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 650 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 650 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 123 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.57e+00 pdb=" NE ARG B 123 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 123 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 123 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 123 " -0.010 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1820 2.77 - 3.30: 9133 3.30 - 3.84: 16022 3.84 - 4.37: 18790 4.37 - 4.90: 32838 Nonbonded interactions: 78603 Sorted by model distance: nonbonded pdb=" OD1 ASP A 155 " pdb="CA CA A 901 " model vdw 2.238 2.510 nonbonded pdb=" OD1 ASP B 155 " pdb="CA CA B 901 " model vdw 2.238 2.510 nonbonded pdb=" OD1 ASP B 176 " pdb="CA CA B 901 " model vdw 2.258 2.510 nonbonded pdb=" OD1 ASP A 176 " pdb="CA CA A 901 " model vdw 2.258 2.510 nonbonded pdb=" OD2 ASP A 179 " pdb="CA CA A 902 " model vdw 2.263 2.510 ... (remaining 78598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.250 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10432 Z= 0.316 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.23), 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 TRP 0.010 0.001 TRP A 347 HIS 0.005 0.001 HIS A 202 PHE 0.023 0.002 PHE A 576 TYR 0.011 0.001 TYR C 6 ARG 0.004 0.000 ARG B 374 *********************** 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 : 1.270 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: 0.2687 time to fit residues: 68.2127 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 : 1.250 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.151462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114748 restraints weight = 12341.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117607 restraints weight = 8896.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117816 restraints weight = 7126.146| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10432 Z= 0.208 Angle : 0.549 8.690 14156 Z= 0.287 Chirality : 0.045 0.173 1580 Planarity : 0.006 0.083 1832 Dihedral : 4.400 32.404 1370 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.86 % Allowed : 19.62 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1272 helix: 1.43 (0.36), residues: 228 sheet: 0.52 (0.26), residues: 402 loop : -0.65 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 347 HIS 0.004 0.001 HIS B 202 PHE 0.018 0.002 PHE A 291 TYR 0.006 0.001 TYR A 356 ARG 0.007 0.001 ARG B 8 *********************** 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 197 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.123 Fit side-chains REVERT: A 183 MET cc_start: 0.7982 (ttm) cc_final: 0.7655 (ttm) REVERT: A 438 ASN cc_start: 0.8067 (p0) cc_final: 0.7665 (p0) REVERT: A 639 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7325 (mtm-85) REVERT: B 183 MET cc_start: 0.7993 (ttm) cc_final: 0.7667 (ttm) REVERT: B 346 GLN cc_start: 0.8105 (pm20) cc_final: 0.7904 (pm20) REVERT: B 438 ASN cc_start: 0.8058 (p0) cc_final: 0.7658 (p0) REVERT: B 639 ARG cc_start: 0.7600 (mtt90) cc_final: 0.7316 (mtm-85) outliers start: 33 outliers final: 13 residues processed: 185 average time/residue: 0.2404 time to fit residues: 62.3076 Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 469 VAL 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 50 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.148639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112874 restraints weight = 12590.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114919 restraints weight = 10796.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116132 restraints weight = 7811.829| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10432 Z= 0.258 Angle : 0.553 8.391 14156 Z= 0.286 Chirality : 0.045 0.174 1580 Planarity : 0.005 0.053 1832 Dihedral : 4.419 22.156 1368 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.34 % Allowed : 20.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1272 helix: 1.44 (0.36), residues: 226 sheet: 0.65 (0.26), residues: 402 loop : -0.56 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.004 0.001 HIS B 637 PHE 0.017 0.002 PHE B 583 TYR 0.008 0.001 TYR B 237 ARG 0.003 0.000 ARG B 374 *********************** 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 218 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7852 (mtt-85) REVERT: A 156 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.6658 (ptp-170) REVERT: A 183 MET cc_start: 0.8076 (ttm) cc_final: 0.7873 (ttm) REVERT: A 438 ASN cc_start: 0.8287 (p0) cc_final: 0.7672 (p0) REVERT: A 449 ASP cc_start: 0.7703 (m-30) cc_final: 0.7216 (m-30) REVERT: A 493 SER cc_start: 0.8691 (m) cc_final: 0.8450 (p) REVERT: A 495 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7735 (mtm110) REVERT: A 509 HIS cc_start: 0.8164 (m90) cc_final: 0.7856 (m90) REVERT: A 550 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7660 (ttt90) REVERT: A 551 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7321 (tm-30) REVERT: A 639 ARG cc_start: 0.7607 (mtt90) cc_final: 0.7113 (mtm-85) REVERT: B 123 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7861 (mtt-85) REVERT: B 156 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6707 (ptp-170) REVERT: B 183 MET cc_start: 0.8075 (ttm) cc_final: 0.7872 (ttm) REVERT: B 438 ASN cc_start: 0.8291 (p0) cc_final: 0.7676 (p0) REVERT: B 449 ASP cc_start: 0.7741 (m-30) cc_final: 0.7262 (m-30) REVERT: B 493 SER cc_start: 0.8658 (m) cc_final: 0.8381 (p) REVERT: B 509 HIS cc_start: 0.8188 (m90) cc_final: 0.7857 (m90) REVERT: B 550 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7662 (ttt90) REVERT: B 551 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7310 (tm-30) REVERT: B 639 ARG cc_start: 0.7565 (mtt90) cc_final: 0.7111 (mtm-85) outliers start: 50 outliers final: 20 residues processed: 202 average time/residue: 0.2765 time to fit residues: 76.8268 Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL 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 284 VAL 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 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 284 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 649 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.153549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113850 restraints weight = 12431.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117548 restraints weight = 7453.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119979 restraints weight = 5449.788| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10432 Z= 0.197 Angle : 0.531 8.403 14156 Z= 0.271 Chirality : 0.044 0.159 1580 Planarity : 0.005 0.049 1832 Dihedral : 4.232 21.977 1368 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.30 % Allowed : 21.01 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1272 helix: 1.54 (0.36), residues: 224 sheet: 0.75 (0.26), residues: 402 loop : -0.49 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 347 HIS 0.003 0.001 HIS A 637 PHE 0.013 0.002 PHE B 291 TYR 0.005 0.001 TYR B 356 ARG 0.005 0.000 ARG B 495 *********************** 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 211 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7742 (mtt-85) REVERT: A 156 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.6679 (ptp-170) REVERT: A 183 MET cc_start: 0.7999 (ttm) cc_final: 0.7783 (ttm) REVERT: A 438 ASN cc_start: 0.8274 (p0) cc_final: 0.7597 (p0) REVERT: A 493 SER cc_start: 0.8673 (m) cc_final: 0.8427 (p) REVERT: A 509 HIS cc_start: 0.8161 (m90) cc_final: 0.7793 (m90) REVERT: A 550 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7532 (ttt90) REVERT: A 551 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7278 (tm-30) REVERT: A 576 PHE cc_start: 0.7360 (m-80) cc_final: 0.6990 (m-80) REVERT: A 639 ARG cc_start: 0.7635 (mtt90) cc_final: 0.7215 (mtm-85) REVERT: B 123 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7757 (mtt-85) REVERT: B 156 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.6689 (ptp-170) REVERT: B 183 MET cc_start: 0.8000 (ttm) cc_final: 0.7777 (ttm) REVERT: B 438 ASN cc_start: 0.8283 (p0) cc_final: 0.7676 (p0) REVERT: B 493 SER cc_start: 0.8651 (m) cc_final: 0.8374 (p) REVERT: B 495 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7625 (mtm110) REVERT: B 547 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8375 (t0) REVERT: B 550 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7509 (ttt90) REVERT: B 551 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7280 (tm-30) REVERT: B 576 PHE cc_start: 0.7353 (m-80) cc_final: 0.6985 (m-80) REVERT: B 639 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7133 (mtm-85) outliers start: 38 outliers final: 19 residues processed: 200 average time/residue: 0.2558 time to fit residues: 69.4015 Evaluate side-chains 189 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 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 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 6 LEU Chi-restraints excluded: chain B residue 18 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.148549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109250 restraints weight = 12804.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112767 restraints weight = 7675.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115030 restraints weight = 5660.790| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10432 Z= 0.373 Angle : 0.619 8.431 14156 Z= 0.318 Chirality : 0.047 0.204 1580 Planarity : 0.005 0.049 1832 Dihedral : 4.821 35.056 1368 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.77 % Allowed : 19.44 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1272 helix: 1.79 (0.38), residues: 212 sheet: 0.48 (0.26), residues: 408 loop : -0.66 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 141 HIS 0.005 0.001 HIS B 637 PHE 0.020 0.003 PHE B 583 TYR 0.011 0.002 TYR A 391 ARG 0.004 0.001 ARG B 374 *********************** 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 218 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8210 (mm-40) cc_final: 0.8001 (mm110) REVERT: A 123 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8006 (mtt-85) REVERT: A 156 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6690 (ptp-170) REVERT: A 438 ASN cc_start: 0.8391 (p0) cc_final: 0.7753 (p0) REVERT: A 449 ASP cc_start: 0.7885 (m-30) cc_final: 0.7582 (m-30) REVERT: A 499 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8018 (ttpt) REVERT: A 503 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8301 (mt-10) REVERT: A 550 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7838 (ttt90) REVERT: A 551 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7332 (tm-30) REVERT: B 123 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8029 (mtt-85) REVERT: B 156 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.6722 (ptp-170) REVERT: B 438 ASN cc_start: 0.8376 (p0) cc_final: 0.7765 (p0) REVERT: B 449 ASP cc_start: 0.7901 (m-30) cc_final: 0.7611 (m-30) REVERT: B 495 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7560 (mtm110) REVERT: B 499 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8016 (ttpt) REVERT: B 503 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8342 (mt-10) REVERT: B 547 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8405 (t0) REVERT: B 550 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7815 (ttt90) REVERT: B 551 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7353 (tm-30) REVERT: B 639 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7166 (mtm-85) outliers start: 55 outliers final: 29 residues processed: 204 average time/residue: 0.2767 time to fit residues: 75.2917 Evaluate side-chains 197 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 42 ILE 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 363 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 42 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3658 r_free = 0.3658 target = 0.150435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112390 restraints weight = 12655.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115000 restraints weight = 8540.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116402 restraints weight = 6095.673| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10432 Z= 0.212 Angle : 0.546 8.392 14156 Z= 0.279 Chirality : 0.045 0.171 1580 Planarity : 0.005 0.046 1832 Dihedral : 4.508 34.747 1368 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.08 % Allowed : 20.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1272 helix: 1.91 (0.38), residues: 212 sheet: 0.70 (0.26), residues: 406 loop : -0.59 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 347 HIS 0.004 0.001 HIS A 637 PHE 0.022 0.002 PHE B 40 TYR 0.006 0.001 TYR B 356 ARG 0.004 0.000 ARG A 374 *********************** 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: 47 poor density : 160 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7748 (ptp90) cc_final: 0.6653 (ptp90) REVERT: A 123 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7819 (mtt-85) REVERT: A 156 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.6603 (ptp-170) REVERT: A 314 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6736 (t80) REVERT: A 438 ASN cc_start: 0.8451 (p0) cc_final: 0.7795 (p0) REVERT: A 499 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7947 (ttpt) REVERT: A 503 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8330 (mt-10) REVERT: A 550 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7664 (ttt90) REVERT: A 551 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7318 (tm-30) REVERT: B 123 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7837 (mtt-85) REVERT: B 156 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.6623 (ptp-170) REVERT: B 314 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.6742 (t80) REVERT: B 438 ASN cc_start: 0.8463 (p0) cc_final: 0.7840 (p0) REVERT: B 449 ASP cc_start: 0.7827 (m-30) cc_final: 0.7513 (m-30) REVERT: B 495 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6937 (mtm110) REVERT: B 499 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7952 (ttpt) REVERT: B 503 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8310 (mt-10) REVERT: B 547 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8312 (t0) REVERT: B 550 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7649 (ttt90) REVERT: B 551 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7327 (tm-30) outliers start: 47 outliers final: 27 residues processed: 194 average time/residue: 0.2758 time to fit residues: 71.7300 Evaluate side-chains 195 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 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 393 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain B residue 42 ILE 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 363 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111419 restraints weight = 12721.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115113 restraints weight = 7538.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117312 restraints weight = 5498.872| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10432 Z= 0.209 Angle : 0.546 8.156 14156 Z= 0.279 Chirality : 0.045 0.167 1580 Planarity : 0.005 0.045 1832 Dihedral : 4.422 34.459 1368 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.08 % Allowed : 21.09 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1272 helix: 1.93 (0.38), residues: 214 sheet: 0.80 (0.26), residues: 406 loop : -0.54 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 347 HIS 0.004 0.001 HIS B 637 PHE 0.022 0.002 PHE A 40 TYR 0.006 0.001 TYR A 391 ARG 0.004 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7847 (mmt) cc_final: 0.7261 (mmt) REVERT: A 123 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7787 (mtt-85) REVERT: A 156 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.6758 (ptp-170) REVERT: A 314 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 318 ASP cc_start: 0.8380 (p0) cc_final: 0.7967 (t70) REVERT: A 438 ASN cc_start: 0.8351 (p0) cc_final: 0.7735 (p0) REVERT: A 499 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7967 (ttpt) REVERT: A 503 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8316 (mt-10) REVERT: A 550 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7663 (ttt90) REVERT: A 551 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7343 (tm-30) REVERT: B 80 MET cc_start: 0.7936 (mmt) cc_final: 0.7480 (mmt) REVERT: B 123 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7808 (mtt-85) REVERT: B 156 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6727 (ptp-170) REVERT: B 314 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6784 (t80) REVERT: B 318 ASP cc_start: 0.8375 (p0) cc_final: 0.7959 (t70) REVERT: B 438 ASN cc_start: 0.8323 (p0) cc_final: 0.7695 (p0) REVERT: B 495 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6817 (mtm110) REVERT: B 499 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7985 (ttpt) REVERT: B 503 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8315 (mt-10) REVERT: B 547 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 550 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7636 (ttt90) REVERT: B 551 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7373 (tm-30) outliers start: 47 outliers final: 28 residues processed: 191 average time/residue: 0.2778 time to fit residues: 71.3706 Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 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 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 7 ILE 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 313 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.153887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114192 restraints weight = 12600.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117846 restraints weight = 7551.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120035 restraints weight = 5533.770| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10432 Z= 0.194 Angle : 0.539 8.105 14156 Z= 0.274 Chirality : 0.044 0.160 1580 Planarity : 0.005 0.048 1832 Dihedral : 4.330 32.893 1368 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.47 % Allowed : 20.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1272 helix: 2.00 (0.38), residues: 214 sheet: 0.92 (0.26), residues: 406 loop : -0.47 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 347 HIS 0.004 0.001 HIS B 637 PHE 0.023 0.002 PHE A 40 TYR 0.006 0.001 TYR B 391 ARG 0.004 0.000 ARG A 374 *********************** 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 201 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8001 (mmt) cc_final: 0.7507 (mmt) REVERT: A 123 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7741 (mtt-85) REVERT: A 156 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.6683 (ptp-170) REVERT: A 269 ILE cc_start: 0.8203 (tp) cc_final: 0.7985 (tt) REVERT: A 314 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6775 (t80) REVERT: A 318 ASP cc_start: 0.8360 (p0) cc_final: 0.7931 (t70) REVERT: A 438 ASN cc_start: 0.8369 (p0) cc_final: 0.7737 (p0) REVERT: A 499 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7998 (ttpt) REVERT: A 503 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8049 (mt-10) REVERT: A 507 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8106 (mt-10) REVERT: A 509 HIS cc_start: 0.8105 (m90) cc_final: 0.7673 (m90) REVERT: A 550 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7633 (ttt90) REVERT: A 551 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7327 (tm-30) REVERT: B 80 MET cc_start: 0.7964 (mmt) cc_final: 0.7559 (mmt) REVERT: B 123 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7719 (mtt-85) REVERT: B 156 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.6698 (ptp-170) REVERT: B 269 ILE cc_start: 0.8229 (tp) cc_final: 0.8009 (tt) REVERT: B 314 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6787 (t80) REVERT: B 318 ASP cc_start: 0.8365 (p0) cc_final: 0.7949 (t70) REVERT: B 438 ASN cc_start: 0.8338 (p0) cc_final: 0.7713 (p0) REVERT: B 495 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7222 (mtm110) REVERT: B 499 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8013 (ttpt) REVERT: B 503 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8325 (mt-10) REVERT: B 509 HIS cc_start: 0.8094 (m90) cc_final: 0.7609 (m90) REVERT: B 547 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8342 (t0) REVERT: B 550 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7631 (ttt90) REVERT: B 551 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7345 (tm-30) outliers start: 40 outliers final: 25 residues processed: 191 average time/residue: 0.3026 time to fit residues: 77.9996 Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 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 402 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 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 363 THR 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 2 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.152654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113229 restraints weight = 12867.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116814 restraints weight = 7611.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119256 restraints weight = 5569.685| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10432 Z= 0.262 Angle : 0.576 7.971 14156 Z= 0.294 Chirality : 0.045 0.178 1580 Planarity : 0.005 0.054 1832 Dihedral : 4.543 37.029 1368 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.99 % Allowed : 20.31 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1272 helix: 1.62 (0.37), residues: 226 sheet: 0.86 (0.26), residues: 404 loop : -0.57 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS B 637 PHE 0.023 0.002 PHE A 40 TYR 0.008 0.001 TYR B 391 ARG 0.008 0.000 ARG A 495 *********************** 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 198 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8025 (mmt) cc_final: 0.7572 (mmt) REVERT: A 123 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7814 (mtt-85) REVERT: A 156 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.6607 (ptp-170) REVERT: A 314 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6186 (t80) REVERT: A 315 GLU cc_start: 0.7886 (mp0) cc_final: 0.7304 (mp0) REVERT: A 318 ASP cc_start: 0.8397 (p0) cc_final: 0.7987 (t70) REVERT: A 383 ARG cc_start: 0.7409 (tpp-160) cc_final: 0.6868 (ttm-80) REVERT: A 438 ASN cc_start: 0.8361 (p0) cc_final: 0.7744 (p0) REVERT: A 499 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7988 (ttpt) REVERT: A 503 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8032 (mt-10) REVERT: A 507 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8151 (mt-10) REVERT: A 550 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7582 (ttt90) REVERT: A 551 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7290 (tm-30) REVERT: B 80 MET cc_start: 0.7979 (mmt) cc_final: 0.7643 (mmt) REVERT: B 123 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7841 (mtt-85) REVERT: B 156 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.6636 (ptp-170) REVERT: B 314 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6204 (t80) REVERT: B 315 GLU cc_start: 0.7895 (mp0) cc_final: 0.7314 (mp0) REVERT: B 318 ASP cc_start: 0.8384 (p0) cc_final: 0.7976 (t70) REVERT: B 383 ARG cc_start: 0.7392 (tpp-160) cc_final: 0.6861 (ttm-80) REVERT: B 438 ASN cc_start: 0.8390 (p0) cc_final: 0.7754 (p0) REVERT: B 495 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7491 (mtm110) REVERT: B 499 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: B 503 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8302 (mt-10) REVERT: B 509 HIS cc_start: 0.8133 (m90) cc_final: 0.7679 (m90) REVERT: B 547 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8315 (t0) REVERT: B 550 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7552 (ttt90) REVERT: B 551 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7296 (tm-30) outliers start: 46 outliers final: 28 residues processed: 189 average time/residue: 0.2790 time to fit residues: 70.8901 Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 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 393 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 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 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 404 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.156066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116913 restraints weight = 12629.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120567 restraints weight = 7577.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122968 restraints weight = 5554.381| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.003 0.029 10432 Z= 0.191 Angle : 0.558 8.003 14156 Z= 0.280 Chirality : 0.044 0.162 1580 Planarity : 0.005 0.051 1832 Dihedral : 4.365 34.544 1368 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.39 % Allowed : 21.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1272 helix: 2.04 (0.38), residues: 214 sheet: 0.89 (0.26), residues: 406 loop : -0.43 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 347 HIS 0.004 0.001 HIS B 637 PHE 0.023 0.001 PHE A 40 TYR 0.005 0.001 TYR B 391 ARG 0.008 0.001 ARG A 495 ********************** 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 194 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7624 (mtt-85) REVERT: A 156 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.6655 (ptp-170) REVERT: A 314 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6325 (t80) REVERT: A 315 GLU cc_start: 0.7863 (mp0) cc_final: 0.7293 (mp0) REVERT: A 318 ASP cc_start: 0.8370 (p0) cc_final: 0.7968 (t70) REVERT: A 383 ARG cc_start: 0.7351 (tpp-160) cc_final: 0.6827 (ttm-80) REVERT: A 438 ASN cc_start: 0.8298 (p0) cc_final: 0.7677 (p0) REVERT: A 499 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7965 (ttpt) REVERT: A 503 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8029 (mt-10) REVERT: A 507 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8159 (mt-10) REVERT: A 550 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7607 (ttt90) REVERT: A 551 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7293 (tm-30) REVERT: B 123 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7733 (mtt-85) REVERT: B 156 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.6760 (ptp-170) REVERT: B 314 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 315 GLU cc_start: 0.7868 (mp0) cc_final: 0.7299 (mp0) REVERT: B 318 ASP cc_start: 0.8384 (p0) cc_final: 0.8001 (t70) REVERT: B 383 ARG cc_start: 0.7346 (tpp-160) cc_final: 0.6827 (ttm-80) REVERT: B 438 ASN cc_start: 0.8321 (p0) cc_final: 0.7690 (p0) REVERT: B 495 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7490 (mtm110) REVERT: B 499 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7993 (ttpt) REVERT: B 503 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8292 (mt-10) REVERT: B 509 HIS cc_start: 0.8055 (m90) cc_final: 0.7808 (m90) REVERT: B 550 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7476 (ttt90) REVERT: B 551 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7320 (tm-30) outliers start: 39 outliers final: 25 residues processed: 186 average time/residue: 0.2693 time to fit residues: 67.6316 Evaluate side-chains 188 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 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 314 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 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 363 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 404 LEU 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 550 ARG Chi-restraints excluded: chain B residue 649 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115658 restraints weight = 12557.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120189 restraints weight = 8133.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121258 restraints weight = 5051.924| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10432 Z= 0.203 Angle : 0.567 7.961 14156 Z= 0.285 Chirality : 0.044 0.162 1580 Planarity : 0.005 0.052 1832 Dihedral : 4.343 33.591 1368 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.04 % Allowed : 21.88 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1272 helix: 1.70 (0.37), residues: 226 sheet: 1.00 (0.26), residues: 402 loop : -0.50 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 141 HIS 0.004 0.001 HIS B 637 PHE 0.023 0.002 PHE A 40 TYR 0.006 0.001 TYR A 391 ARG 0.005 0.000 ARG B 495 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3148.61 seconds wall clock time: 57 minutes 25.66 seconds (3445.66 seconds total)