Starting phenix.real_space_refine on Thu May 1 04:32:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8v_19012/05_2025/8r8v_19012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8v_19012/05_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_19012/05_2025/8r8v_19012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8v_19012/05_2025/8r8v_19012.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8v_19012/05_2025/8r8v_19012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8v_19012/05_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-5669/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: 6.59, per 1000 atoms: 0.65 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: 2.67 Conformation dependent library (CDL) restraints added in 1.2 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: 1.46 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: 3.62 Time building geometry restraints manager: 3.12 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: 1.730 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.040 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 10434 Z= 0.347 Angle : 0.717 7.444 14156 Z= 0.456 Chirality : 0.054 0.267 1580 Planarity : 0.009 0.127 1832 Dihedral : 15.813 88.546 3888 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.61 % Allowed : 20.83 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.11452 ( 368) hydrogen bonds : angle 5.90691 ( 930) covalent geometry : bond 0.00483 (10432) covalent geometry : angle 0.71714 (14156) Misc. bond : bond 0.09536 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 1.163 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: 0.2574 time to fit residues: 65.2907 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 : 1.047 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.151536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.114868 restraints weight = 12340.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117872 restraints weight = 8923.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.118060 restraints weight = 7109.684| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 10434 Z= 0.135 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 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 368) hydrogen bonds : angle 4.94960 ( 930) covalent geometry : bond 0.00322 (10432) covalent geometry : angle 0.54919 (14156) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.362 Fit side-chains REVERT: A 183 MET cc_start: 0.7986 (ttm) cc_final: 0.7659 (ttm) REVERT: A 438 ASN cc_start: 0.8064 (p0) cc_final: 0.7660 (p0) REVERT: A 639 ARG cc_start: 0.7613 (mtt90) cc_final: 0.7328 (mtm-85) REVERT: B 183 MET cc_start: 0.7993 (ttm) cc_final: 0.7668 (ttm) REVERT: B 346 GLN cc_start: 0.8107 (pm20) cc_final: 0.7905 (pm20) REVERT: B 438 ASN cc_start: 0.8055 (p0) cc_final: 0.7657 (p0) REVERT: B 639 ARG cc_start: 0.7601 (mtt90) cc_final: 0.7318 (mtm-85) outliers start: 33 outliers final: 13 residues processed: 185 average time/residue: 0.2732 time to fit residues: 71.7571 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 : 1.061 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 3.9990 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: 0.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.145578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109534 restraints weight = 12771.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110768 restraints weight = 11389.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112504 restraints weight = 8236.329| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10434 Z= 0.241 Angle : 0.621 8.601 14156 Z= 0.322 Chirality : 0.048 0.207 1580 Planarity : 0.005 0.054 1832 Dihedral : 4.839 29.789 1368 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.77 % Allowed : 20.57 % Favored : 74.65 % 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: 0.06 (0.24), residues: 1272 helix: 1.32 (0.36), residues: 226 sheet: 0.49 (0.26), residues: 404 loop : -0.71 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 141 HIS 0.004 0.001 HIS A 637 PHE 0.020 0.003 PHE B 583 TYR 0.012 0.002 TYR B 237 ARG 0.004 0.001 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 368) hydrogen bonds : angle 5.15147 ( 930) covalent geometry : bond 0.00594 (10432) covalent geometry : angle 0.62068 (14156) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7993 (mtt-85) REVERT: A 156 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.6513 (ptp-170) REVERT: A 438 ASN cc_start: 0.8379 (p0) cc_final: 0.7805 (p0) REVERT: A 449 ASP cc_start: 0.7748 (m-30) cc_final: 0.7513 (m-30) REVERT: A 495 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7701 (mtm110) REVERT: A 550 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7836 (ttm170) REVERT: A 551 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7243 (tm-30) REVERT: A 639 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7117 (mtm-85) REVERT: B 123 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7949 (mtt-85) REVERT: B 156 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6537 (ptp-170) REVERT: B 438 ASN cc_start: 0.8370 (p0) cc_final: 0.7772 (p0) REVERT: B 449 ASP cc_start: 0.7780 (m-30) cc_final: 0.7554 (m-30) REVERT: B 493 SER cc_start: 0.8755 (m) cc_final: 0.8531 (p) REVERT: B 503 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8311 (mt-10) REVERT: B 550 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7795 (ttm170) REVERT: B 551 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7272 (tm-30) REVERT: B 639 ARG cc_start: 0.7571 (mtt90) cc_final: 0.7084 (mtm-85) outliers start: 55 outliers final: 21 residues processed: 199 average time/residue: 0.2812 time to fit residues: 76.2026 Evaluate side-chains 183 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 9 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 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 635 THR Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 649 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 0.0170 chunk 127 optimal weight: 0.0060 chunk 72 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.155146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.117404 restraints weight = 12393.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.121742 restraints weight = 8426.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123292 restraints weight = 5342.113| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10434 Z= 0.099 Angle : 0.519 8.635 14156 Z= 0.264 Chirality : 0.043 0.147 1580 Planarity : 0.004 0.048 1832 Dihedral : 4.238 23.838 1368 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.56 % Allowed : 20.75 % 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: 0.44 (0.24), residues: 1272 helix: 1.78 (0.37), residues: 216 sheet: 0.77 (0.26), residues: 400 loop : -0.50 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 347 HIS 0.004 0.001 HIS A 202 PHE 0.013 0.001 PHE A 407 TYR 0.005 0.001 TYR D 6 ARG 0.005 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 368) hydrogen bonds : angle 4.70741 ( 930) covalent geometry : bond 0.00225 (10432) covalent geometry : angle 0.51900 (14156) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7735 (mtt-85) REVERT: A 156 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6779 (ptp-170) REVERT: A 438 ASN cc_start: 0.8099 (p0) cc_final: 0.7453 (p0) REVERT: A 550 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7666 (ttt90) REVERT: A 551 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7402 (tm-30) REVERT: A 576 PHE cc_start: 0.7283 (m-80) cc_final: 0.6926 (m-80) REVERT: B 123 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7747 (mtt-85) REVERT: B 156 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6786 (ptp-170) REVERT: B 438 ASN cc_start: 0.8099 (p0) cc_final: 0.7442 (p0) REVERT: B 493 SER cc_start: 0.8681 (m) cc_final: 0.8461 (p) REVERT: B 495 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7324 (mtm110) REVERT: B 547 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8373 (t0) REVERT: B 551 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7426 (tm-30) REVERT: B 576 PHE cc_start: 0.7277 (m-80) cc_final: 0.6921 (m-80) REVERT: B 639 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7153 (mtm-85) outliers start: 41 outliers final: 16 residues processed: 198 average time/residue: 0.2584 time to fit residues: 69.3184 Evaluate side-chains 179 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 6 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 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 547 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.150390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110808 restraints weight = 12704.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.114348 restraints weight = 7660.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116738 restraints weight = 5634.057| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10434 Z= 0.191 Angle : 0.585 8.329 14156 Z= 0.299 Chirality : 0.046 0.190 1580 Planarity : 0.005 0.048 1832 Dihedral : 4.590 32.396 1368 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.99 % Allowed : 20.66 % 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: 0.35 (0.24), residues: 1272 helix: 1.91 (0.38), residues: 214 sheet: 0.63 (0.26), residues: 404 loop : -0.58 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 141 HIS 0.005 0.001 HIS A 637 PHE 0.018 0.002 PHE B 583 TYR 0.009 0.001 TYR B 391 ARG 0.004 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 368) hydrogen bonds : angle 4.92348 ( 930) covalent geometry : bond 0.00472 (10432) covalent geometry : angle 0.58473 (14156) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7861 (mtt-85) REVERT: A 156 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.6568 (ptp-170) REVERT: A 183 MET cc_start: 0.8181 (ttm) cc_final: 0.7920 (ttm) REVERT: A 438 ASN cc_start: 0.8488 (p0) cc_final: 0.7841 (p0) REVERT: A 449 ASP cc_start: 0.7803 (m-30) cc_final: 0.7487 (m-30) REVERT: A 503 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8182 (mt-10) REVERT: A 507 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8003 (mt-10) REVERT: A 550 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7641 (ttt90) REVERT: A 551 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7274 (tm-30) REVERT: B 123 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7880 (mtt-85) REVERT: B 156 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.6592 (ptp-170) REVERT: B 183 MET cc_start: 0.8186 (ttm) cc_final: 0.7926 (ttm) REVERT: B 314 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6758 (t80) REVERT: B 438 ASN cc_start: 0.8487 (p0) cc_final: 0.7874 (p0) REVERT: B 449 ASP cc_start: 0.7817 (m-30) cc_final: 0.7506 (m-30) REVERT: B 495 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7455 (mtm110) REVERT: B 503 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8293 (mt-10) REVERT: B 547 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8418 (t0) REVERT: B 550 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7625 (ttt90) REVERT: B 551 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7298 (tm-30) outliers start: 46 outliers final: 26 residues processed: 186 average time/residue: 0.2936 time to fit residues: 73.9751 Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 269 ILE Chi-restraints excluded: chain A residue 284 VAL 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 530 LEU 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 48 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 530 LEU 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: 6.9990 chunk 103 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113267 restraints weight = 12546.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116944 restraints weight = 7432.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119405 restraints weight = 5427.770| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10434 Z= 0.119 Angle : 0.531 8.252 14156 Z= 0.271 Chirality : 0.044 0.161 1580 Planarity : 0.004 0.046 1832 Dihedral : 4.309 30.859 1368 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.73 % Allowed : 21.01 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.24), residues: 1272 helix: 2.00 (0.38), residues: 214 sheet: 0.87 (0.26), residues: 404 loop : -0.47 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 347 HIS 0.003 0.001 HIS B 637 PHE 0.022 0.001 PHE A 40 TYR 0.005 0.001 TYR B 391 ARG 0.004 0.000 ARG B 374 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 368) hydrogen bonds : angle 4.68421 ( 930) covalent geometry : bond 0.00286 (10432) covalent geometry : angle 0.53082 (14156) Misc. bond : bond 0.00011 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7684 (ptp90) cc_final: 0.6570 (ptp90) REVERT: A 80 MET cc_start: 0.7637 (mmm) cc_final: 0.7141 (mmt) REVERT: A 123 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7771 (mtt-85) REVERT: A 156 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.6715 (ptp-170) REVERT: A 175 GLU cc_start: 0.7955 (mp0) cc_final: 0.7672 (mt-10) REVERT: A 314 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 438 ASN cc_start: 0.8332 (p0) cc_final: 0.7695 (p0) REVERT: A 503 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8174 (mt-10) REVERT: A 507 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7967 (mt-10) REVERT: A 550 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7577 (ttt90) REVERT: A 551 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7333 (tm-30) REVERT: B 80 MET cc_start: 0.7885 (mmt) cc_final: 0.7413 (mmt) REVERT: B 123 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7785 (mtt-85) REVERT: B 156 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.6726 (ptp-170) REVERT: B 175 GLU cc_start: 0.7958 (mp0) cc_final: 0.7682 (mt-10) REVERT: B 314 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6235 (t80) REVERT: B 315 GLU cc_start: 0.7833 (mp0) cc_final: 0.7255 (mp0) REVERT: B 438 ASN cc_start: 0.8341 (p0) cc_final: 0.7715 (p0) REVERT: B 495 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6878 (mtm110) REVERT: B 507 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8056 (mt-10) REVERT: B 547 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8370 (t0) REVERT: B 550 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7583 (ttt90) REVERT: B 551 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7338 (tm-30) outliers start: 43 outliers final: 24 residues processed: 191 average time/residue: 0.3058 time to fit residues: 79.5641 Evaluate side-chains 193 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.152718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114793 restraints weight = 12688.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119044 restraints weight = 8297.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120419 restraints weight = 5241.121| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10434 Z= 0.138 Angle : 0.548 7.982 14156 Z= 0.280 Chirality : 0.045 0.166 1580 Planarity : 0.004 0.044 1832 Dihedral : 4.368 31.657 1368 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.39 % Allowed : 20.75 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.24), residues: 1272 helix: 1.99 (0.38), residues: 214 sheet: 0.91 (0.26), residues: 406 loop : -0.48 (0.24), residues: 652 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 0.021 0.002 PHE B 40 TYR 0.007 0.001 TYR B 391 ARG 0.004 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 368) hydrogen bonds : angle 4.64207 ( 930) covalent geometry : bond 0.00337 (10432) covalent geometry : angle 0.54752 (14156) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7634 (mmm) cc_final: 0.7198 (mmt) REVERT: A 123 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7679 (mtt-85) REVERT: A 156 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.6591 (ptp-170) REVERT: A 314 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6754 (t80) REVERT: A 438 ASN cc_start: 0.8434 (p0) cc_final: 0.7773 (p0) REVERT: A 503 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8202 (mt-10) REVERT: A 507 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8062 (mt-10) REVERT: A 550 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7683 (ttt90) REVERT: A 551 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7342 (tm-30) REVERT: B 80 MET cc_start: 0.7936 (mmt) cc_final: 0.7459 (mmt) REVERT: B 123 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7784 (mtt-85) REVERT: B 156 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.6616 (ptp-170) REVERT: B 269 ILE cc_start: 0.8183 (tp) cc_final: 0.7952 (tt) REVERT: B 438 ASN cc_start: 0.8432 (p0) cc_final: 0.7777 (p0) REVERT: B 495 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6796 (mtm110) REVERT: B 503 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8172 (mt-10) REVERT: B 507 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8068 (mt-10) REVERT: B 509 HIS cc_start: 0.8231 (m90) cc_final: 0.7742 (m90) REVERT: B 547 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8373 (t0) REVERT: B 550 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7624 (ttt90) REVERT: B 551 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7355 (tm-30) outliers start: 39 outliers final: 29 residues processed: 184 average time/residue: 0.2661 time to fit residues: 65.9603 Evaluate side-chains 186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 70 LEU 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 401 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 530 LEU 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 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 530 LEU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.154882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115457 restraints weight = 12606.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119151 restraints weight = 7453.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121650 restraints weight = 5421.693| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10434 Z= 0.123 Angle : 0.540 7.935 14156 Z= 0.275 Chirality : 0.044 0.159 1580 Planarity : 0.004 0.043 1832 Dihedral : 4.281 30.497 1368 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.82 % Allowed : 20.05 % Favored : 76.13 % 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: 0.66 (0.24), residues: 1272 helix: 2.06 (0.38), residues: 214 sheet: 0.97 (0.26), residues: 406 loop : -0.44 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 347 HIS 0.003 0.001 HIS B 637 PHE 0.022 0.001 PHE B 40 TYR 0.006 0.001 TYR D 6 ARG 0.004 0.000 ARG B 374 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 368) hydrogen bonds : angle 4.57394 ( 930) covalent geometry : bond 0.00297 (10432) covalent geometry : angle 0.53967 (14156) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7547 (mmm) cc_final: 0.7321 (mmt) REVERT: A 123 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7660 (mtt-85) REVERT: A 156 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6730 (ptp-170) REVERT: A 314 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6771 (t80) REVERT: A 318 ASP cc_start: 0.8331 (p0) cc_final: 0.7915 (t70) REVERT: A 438 ASN cc_start: 0.8334 (p0) cc_final: 0.7675 (p0) REVERT: A 503 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8183 (mt-10) REVERT: A 507 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8052 (mt-10) REVERT: A 509 HIS cc_start: 0.8049 (m90) cc_final: 0.7665 (m90) REVERT: A 550 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7651 (ttt90) REVERT: A 551 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7322 (tm-30) REVERT: B 80 MET cc_start: 0.7993 (mmt) cc_final: 0.7726 (mmt) REVERT: B 123 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7629 (mtt-85) REVERT: B 156 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.6736 (ptp-170) REVERT: B 269 ILE cc_start: 0.8221 (tp) cc_final: 0.8016 (tt) REVERT: B 314 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6512 (t80) REVERT: B 438 ASN cc_start: 0.8364 (p0) cc_final: 0.7712 (p0) REVERT: B 495 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7355 (mtm110) REVERT: B 503 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8170 (mt-10) REVERT: B 507 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7975 (mt-10) REVERT: B 509 HIS cc_start: 0.8167 (m90) cc_final: 0.7666 (m90) REVERT: B 547 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8309 (t0) REVERT: B 550 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7610 (ttt90) REVERT: B 551 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7333 (tm-30) outliers start: 44 outliers final: 29 residues processed: 191 average time/residue: 0.3008 time to fit residues: 78.0244 Evaluate side-chains 192 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 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 530 LEU 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 48 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 114 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.154236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114807 restraints weight = 12770.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118454 restraints weight = 7488.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120955 restraints weight = 5440.723| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10434 Z= 0.141 Angle : 0.564 8.347 14156 Z= 0.285 Chirality : 0.045 0.166 1580 Planarity : 0.005 0.047 1832 Dihedral : 4.355 31.316 1368 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.56 % Allowed : 20.49 % Favored : 75.95 % 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: 0.66 (0.24), residues: 1272 helix: 2.07 (0.37), residues: 214 sheet: 0.91 (0.26), residues: 408 loop : -0.41 (0.24), residues: 650 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 0.007 0.001 TYR B 391 ARG 0.004 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 368) hydrogen bonds : angle 4.60516 ( 930) covalent geometry : bond 0.00344 (10432) covalent geometry : angle 0.56364 (14156) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7671 (mtt-85) REVERT: A 156 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.6729 (ptp-170) REVERT: A 269 ILE cc_start: 0.8301 (tp) cc_final: 0.8042 (tt) REVERT: A 314 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6212 (t80) REVERT: A 315 GLU cc_start: 0.7760 (mp0) cc_final: 0.7238 (mp0) REVERT: A 318 ASP cc_start: 0.8342 (p0) cc_final: 0.7996 (t70) REVERT: A 383 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.6887 (ttm-80) REVERT: A 438 ASN cc_start: 0.8318 (p0) cc_final: 0.7661 (p0) REVERT: A 503 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8157 (mt-10) REVERT: A 507 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8068 (mt-10) REVERT: A 509 HIS cc_start: 0.8039 (m90) cc_final: 0.7735 (m90) REVERT: A 550 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7639 (ttt90) REVERT: A 551 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7393 (tm-30) REVERT: B 80 MET cc_start: 0.7987 (mmt) cc_final: 0.7723 (mmt) REVERT: B 123 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7701 (mtt-85) REVERT: B 156 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.6738 (ptp-170) REVERT: B 318 ASP cc_start: 0.8340 (p0) cc_final: 0.8002 (t70) REVERT: B 383 ARG cc_start: 0.7415 (tpp-160) cc_final: 0.6879 (ttm-80) REVERT: B 438 ASN cc_start: 0.8314 (p0) cc_final: 0.7675 (p0) REVERT: B 495 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7403 (mtm110) REVERT: B 503 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8186 (mt-10) REVERT: B 507 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8041 (mt-10) REVERT: B 509 HIS cc_start: 0.8107 (m90) cc_final: 0.7773 (m90) REVERT: B 547 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8314 (t0) REVERT: B 550 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7593 (ttt90) REVERT: B 551 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7382 (tm-30) outliers start: 41 outliers final: 30 residues processed: 184 average time/residue: 0.4070 time to fit residues: 101.6878 Evaluate side-chains 189 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 ILE 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 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 48 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 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 530 LEU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 550 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 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 = 0.3718 r_free = 0.3718 target = 0.155238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116102 restraints weight = 12654.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119673 restraints weight = 7725.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122020 restraints weight = 5690.818| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10434 Z= 0.163 Angle : 0.588 8.089 14156 Z= 0.297 Chirality : 0.045 0.178 1580 Planarity : 0.005 0.053 1832 Dihedral : 4.548 35.890 1368 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.30 % Allowed : 21.18 % 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: 0.57 (0.24), residues: 1272 helix: 2.02 (0.37), residues: 214 sheet: 0.83 (0.26), residues: 408 loop : -0.46 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 A 391 ARG 0.010 0.001 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 368) hydrogen bonds : angle 4.70199 ( 930) covalent geometry : bond 0.00402 (10432) covalent geometry : angle 0.58808 (14156) Misc. bond : bond 0.00019 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7820 (mtt-85) REVERT: A 156 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.6796 (ptp-170) REVERT: A 164 MET cc_start: 0.8161 (ttm) cc_final: 0.7907 (ttp) REVERT: A 314 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6759 (t80) REVERT: A 318 ASP cc_start: 0.8330 (p0) cc_final: 0.8012 (t70) REVERT: A 383 ARG cc_start: 0.7409 (tpp-160) cc_final: 0.6904 (ttm-80) REVERT: A 438 ASN cc_start: 0.8208 (p0) cc_final: 0.7624 (p0) REVERT: A 503 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8109 (mt-10) REVERT: A 550 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7723 (ttt90) REVERT: A 551 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7375 (tm-30) REVERT: B 80 MET cc_start: 0.7959 (mmt) cc_final: 0.7736 (mmt) REVERT: B 123 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7853 (mtt-85) REVERT: B 156 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.6821 (ptp-170) REVERT: B 318 ASP cc_start: 0.8320 (p0) cc_final: 0.8031 (t70) REVERT: B 383 ARG cc_start: 0.7422 (tpp-160) cc_final: 0.6911 (ttm-80) REVERT: B 438 ASN cc_start: 0.8197 (p0) cc_final: 0.7586 (p0) REVERT: B 495 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7481 (mtm110) REVERT: B 550 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7684 (ttt90) REVERT: B 551 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7419 (tm-30) outliers start: 38 outliers final: 28 residues processed: 179 average time/residue: 0.2553 time to fit residues: 62.1181 Evaluate side-chains 183 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 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 404 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 530 LEU 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 48 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 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 530 LEU Chi-restraints excluded: chain B residue 550 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 445 GLN B 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.155161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116545 restraints weight = 12592.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120109 restraints weight = 7625.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.122389 restraints weight = 5606.493| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10434 Z= 0.166 Angle : 0.599 7.998 14156 Z= 0.303 Chirality : 0.046 0.176 1580 Planarity : 0.005 0.052 1832 Dihedral : 4.616 38.951 1368 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.39 % Allowed : 21.70 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.24), residues: 1272 helix: 1.95 (0.37), residues: 214 sheet: 0.80 (0.26), residues: 408 loop : -0.47 (0.24), residues: 650 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 0.022 0.002 PHE A 40 TYR 0.009 0.001 TYR A 391 ARG 0.007 0.001 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 368) hydrogen bonds : angle 4.73411 ( 930) covalent geometry : bond 0.00409 (10432) covalent geometry : angle 0.59909 (14156) Misc. bond : bond 0.00019 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.99 seconds wall clock time: 65 minutes 13.30 seconds (3913.30 seconds total)