Starting phenix.real_space_refine on Tue Jul 29 10:55:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ysz_39566/07_2025/8ysz_39566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ysz_39566/07_2025/8ysz_39566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ysz_39566/07_2025/8ysz_39566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ysz_39566/07_2025/8ysz_39566.map" model { file = "/net/cci-nas-00/data/ceres_data/8ysz_39566/07_2025/8ysz_39566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ysz_39566/07_2025/8ysz_39566.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 7081 2.51 5 N 1922 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11170 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 244 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain breaks: 1 Chain: "A" Number of atoms: 6408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6408 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 41, 'TRANS': 755} Chain breaks: 9 Chain: "B" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3874 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 25, 'TRANS': 451} Chain breaks: 10 Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain breaks: 1 Chain: "E" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain breaks: 1 Time building chain proxies: 8.78, per 1000 atoms: 0.79 Number of scatterers: 11170 At special positions: 0 Unit cell: (90.42, 114.84, 173.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 2090 8.00 N 1922 7.00 C 7081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 60 " distance=2.04 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 215 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 328 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 360 " distance=2.04 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 51 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 24 sheets defined 16.5% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'D' and resid 11 through 22 removed outlier: 4.140A pdb=" N LEU D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.930A pdb=" N ARG A 46 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.682A pdb=" N ILE A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.644A pdb=" N CYS A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.537A pdb=" N ILE A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 891 through 896 removed outlier: 4.204A pdb=" N GLU A 896 " --> pdb=" O HIS A 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.543A pdb=" N LEU B 357 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 386 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.473A pdb=" N PHE B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 462 through 473 removed outlier: 3.501A pdb=" N LYS B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 removed outlier: 4.309A pdb=" N GLN B 479 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 721 through 741 removed outlier: 3.651A pdb=" N PHE B 741 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 895 removed outlier: 3.888A pdb=" N ALA B 894 " --> pdb=" O LYS B 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.741A pdb=" N VAL C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.528A pdb=" N LEU C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 52 through 57 removed outlier: 3.528A pdb=" N LEU E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 41 removed outlier: 7.247A pdb=" N GLU A 33 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A 56 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS A 35 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY A 58 " --> pdb=" O CYS A 35 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY A 37 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 60 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP A 39 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 62 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG A 41 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 41 removed outlier: 7.247A pdb=" N GLU A 33 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A 56 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS A 35 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY A 58 " --> pdb=" O CYS A 35 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY A 37 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 60 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP A 39 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 62 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG A 41 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A 87 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY A 58 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N LEU A 89 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 60 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE A 91 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 62 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 88 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE A 123 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 90 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ARG A 145 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 121 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A 147 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE A 123 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 144 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL A 173 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 146 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 243 removed outlier: 7.170A pdb=" N ASN A 242 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N CYS A 252 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 281 removed outlier: 6.377A pdb=" N HIS A 274 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 348 removed outlier: 6.249A pdb=" N LYS A 346 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE A 454 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 428 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N HIS A 456 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 430 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 453 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 502 through 507 Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 561 Processing sheet with id=AB1, first strand: chain 'A' and resid 557 through 561 Processing sheet with id=AB2, first strand: chain 'A' and resid 626 through 634 removed outlier: 5.222A pdb=" N ASP A 627 " --> pdb=" O LYS A 643 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 643 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN A 633 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 789 removed outlier: 3.833A pdb=" N GLU A 787 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 657 " --> pdb=" O GLU A 787 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 871 through 872 removed outlier: 3.685A pdb=" N LEU A 871 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 874 through 875 Processing sheet with id=AB6, first strand: chain 'A' and resid 907 through 911 Processing sheet with id=AB7, first strand: chain 'B' and resid 338 through 346 removed outlier: 7.457A pdb=" N VAL B 362 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS B 340 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN B 364 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 342 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N SER B 366 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY B 344 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 390 through 393 removed outlier: 7.103A pdb=" N ILE B 391 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 395 through 398 removed outlier: 5.497A pdb=" N LYS B 452 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 427 " --> pdb=" O LYS B 452 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 502 through 506 Processing sheet with id=AC2, first strand: chain 'B' and resid 557 through 561 removed outlier: 3.614A pdb=" N GLY B 529 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 629 through 634 removed outlier: 6.193A pdb=" N GLN B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 638 " --> pdb=" O ILE B 797 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 786 through 789 removed outlier: 4.619A pdb=" N ALA B 812 " --> pdb=" O SER B 823 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 823 " --> pdb=" O ALA B 812 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 786 through 789 Processing sheet with id=AC6, first strand: chain 'B' and resid 845 through 849 removed outlier: 3.517A pdb=" N THR B 846 " --> pdb=" O MET B 858 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 648 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: 3.70 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2008 1.32 - 1.45: 3019 1.45 - 1.57: 6297 1.57 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 11417 Sorted by residual: bond pdb=" CA PRO B 576 " pdb=" C PRO B 576 " ideal model delta sigma weight residual 1.521 1.470 0.051 1.19e-02 7.06e+03 1.87e+01 bond pdb=" N PRO B 576 " pdb=" CA PRO B 576 " ideal model delta sigma weight residual 1.466 1.421 0.044 1.21e-02 6.83e+03 1.34e+01 bond pdb=" C PRO B 576 " pdb=" O PRO B 576 " ideal model delta sigma weight residual 1.233 1.199 0.034 1.21e-02 6.83e+03 7.96e+00 bond pdb=" N GLY A 27 " pdb=" CA GLY A 27 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.11e+00 bond pdb=" CA PRO B 576 " pdb=" CB PRO B 576 " ideal model delta sigma weight residual 1.533 1.500 0.033 1.47e-02 4.63e+03 4.98e+00 ... (remaining 11412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 14935 1.62 - 3.23: 442 3.23 - 4.85: 56 4.85 - 6.47: 9 6.47 - 8.08: 1 Bond angle restraints: 15443 Sorted by residual: angle pdb=" CA PRO B 576 " pdb=" C PRO B 576 " pdb=" O PRO B 576 " ideal model delta sigma weight residual 121.95 116.02 5.93 1.25e+00 6.40e-01 2.25e+01 angle pdb=" CA PRO B 576 " pdb=" C PRO B 576 " pdb=" N GLY B 577 " ideal model delta sigma weight residual 115.04 121.39 -6.35 1.35e+00 5.49e-01 2.21e+01 angle pdb=" N TYR A 806 " pdb=" CA TYR A 806 " pdb=" C TYR A 806 " ideal model delta sigma weight residual 108.34 113.50 -5.16 1.31e+00 5.83e-01 1.55e+01 angle pdb=" N ASN A 42 " pdb=" CA ASN A 42 " pdb=" CB ASN A 42 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N LYS B 511 " pdb=" CA LYS B 511 " pdb=" C LYS B 511 " ideal model delta sigma weight residual 109.06 115.25 -6.19 1.70e+00 3.46e-01 1.32e+01 ... (remaining 15438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6197 17.92 - 35.83: 529 35.83 - 53.75: 115 53.75 - 71.67: 32 71.67 - 89.58: 14 Dihedral angle restraints: 6887 sinusoidal: 2864 harmonic: 4023 Sorted by residual: dihedral pdb=" CB CYS D 21 " pdb=" SG CYS D 21 " pdb=" SG CYS D 60 " pdb=" CB CYS D 60 " ideal model delta sinusoidal sigma weight residual 93.00 13.23 79.77 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS A 268 " pdb=" SG CYS A 268 " pdb=" SG CYS A 280 " pdb=" CB CYS A 280 " ideal model delta sinusoidal sigma weight residual 93.00 168.88 -75.88 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS A 286 " pdb=" SG CYS A 286 " pdb=" SG CYS A 311 " pdb=" CB CYS A 311 " ideal model delta sinusoidal sigma weight residual -86.00 -148.08 62.08 1 1.00e+01 1.00e-02 5.10e+01 ... (remaining 6884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1006 0.029 - 0.058: 459 0.058 - 0.087: 97 0.087 - 0.116: 94 0.116 - 0.146: 26 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE A 84 " pdb=" N ILE A 84 " pdb=" C ILE A 84 " pdb=" CB ILE A 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 122 " pdb=" N ILE A 122 " pdb=" C ILE A 122 " pdb=" CB ILE A 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1679 not shown) Planarity restraints: 1991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 520 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 521 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 873 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" CD GLU B 873 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU B 873 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU B 873 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 575 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO B 576 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 576 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 576 " -0.016 5.00e-02 4.00e+02 ... (remaining 1988 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 143 2.59 - 3.17: 10336 3.17 - 3.75: 16465 3.75 - 4.32: 23790 4.32 - 4.90: 38241 Nonbonded interactions: 88975 Sorted by model distance: nonbonded pdb=" O ARG A 604 " pdb=" OG1 THR A 605 " model vdw 2.017 3.040 nonbonded pdb=" O GLU A 883 " pdb=" OE1 GLU A 883 " model vdw 2.128 3.040 nonbonded pdb=" N GLU A 130 " pdb=" OE1 GLU A 130 " model vdw 2.136 3.120 nonbonded pdb=" NH1 ARG B 801 " pdb=" OE2 GLU B 864 " model vdw 2.198 3.120 nonbonded pdb=" N GLU C 12 " pdb=" OE1 GLU C 12 " model vdw 2.206 3.120 ... (remaining 88970 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 187.930 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.360 Find NCS groups from input model: 0.100 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: 222.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.003 0.051 11441 Z= 0.163 Angle : 0.659 8.084 15491 Z= 0.384 Chirality : 0.041 0.146 1682 Planarity : 0.003 0.034 1991 Dihedral : 14.547 89.585 4211 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.72 % Allowed : 12.36 % Favored : 86.92 % 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: -1.65 (0.23), residues: 1336 helix: -0.64 (0.43), residues: 150 sheet: -1.13 (0.34), residues: 244 loop : -1.21 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 556 HIS 0.007 0.001 HIS A 892 PHE 0.009 0.001 PHE E 19 TYR 0.010 0.001 TYR A 606 ARG 0.004 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.23438 ( 243) hydrogen bonds : angle 9.77880 ( 648) SS BOND : bond 0.00263 ( 24) SS BOND : angle 0.79591 ( 48) covalent geometry : bond 0.00300 (11417) covalent geometry : angle 0.65805 (15443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9294 (pp) cc_final: 0.9059 (mp) REVERT: A 321 MET cc_start: 0.8330 (pmm) cc_final: 0.8096 (pmm) REVERT: B 469 MET cc_start: 0.8630 (tpt) cc_final: 0.8291 (tpp) outliers start: 9 outliers final: 2 residues processed: 78 average time/residue: 0.2372 time to fit residues: 27.5531 Evaluate side-chains 60 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 384 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 482 ASN B 458 ASN B 467 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.084791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.058477 restraints weight = 44160.466| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 4.30 r_work: 0.3022 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11441 Z= 0.273 Angle : 0.730 10.855 15491 Z= 0.379 Chirality : 0.047 0.174 1682 Planarity : 0.004 0.030 1991 Dihedral : 6.023 23.528 1506 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.98 % Favored : 90.94 % Rotamer: Outliers : 2.17 % Allowed : 13.48 % Favored : 84.35 % 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: -1.79 (0.22), residues: 1336 helix: -0.87 (0.40), residues: 160 sheet: -1.48 (0.31), residues: 265 loop : -1.18 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 439 HIS 0.010 0.001 HIS A 802 PHE 0.019 0.002 PHE A 803 TYR 0.018 0.002 TYR A 428 ARG 0.004 0.001 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 243) hydrogen bonds : angle 7.48286 ( 648) SS BOND : bond 0.00389 ( 24) SS BOND : angle 0.97058 ( 48) covalent geometry : bond 0.00614 (11417) covalent geometry : angle 0.72865 (15443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9399 (pp) cc_final: 0.9095 (mp) REVERT: A 431 ASP cc_start: 0.8398 (t0) cc_final: 0.8068 (t0) REVERT: A 601 ASP cc_start: 0.8853 (p0) cc_final: 0.8297 (t0) REVERT: B 543 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 892 HIS cc_start: 0.9342 (OUTLIER) cc_final: 0.8953 (t-170) REVERT: C 17 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8474 (tt) outliers start: 27 outliers final: 11 residues processed: 84 average time/residue: 0.1769 time to fit residues: 24.6493 Evaluate side-chains 65 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 892 HIS Chi-restraints excluded: chain C residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 112 optimal weight: 0.0050 chunk 57 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.086434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.060383 restraints weight = 44991.707| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.37 r_work: 0.3075 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11441 Z= 0.113 Angle : 0.603 9.674 15491 Z= 0.313 Chirality : 0.043 0.145 1682 Planarity : 0.003 0.032 1991 Dihedral : 5.515 23.109 1502 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.81 % Rotamer: Outliers : 2.25 % Allowed : 14.45 % Favored : 83.31 % 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: -1.62 (0.23), residues: 1336 helix: -0.62 (0.40), residues: 160 sheet: -1.30 (0.32), residues: 253 loop : -1.12 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 924 HIS 0.010 0.001 HIS A 654 PHE 0.014 0.001 PHE A 258 TYR 0.011 0.001 TYR B 876 ARG 0.003 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 243) hydrogen bonds : angle 6.85197 ( 648) SS BOND : bond 0.00356 ( 24) SS BOND : angle 0.78627 ( 48) covalent geometry : bond 0.00238 (11417) covalent geometry : angle 0.60240 (15443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9380 (pp) cc_final: 0.9113 (mp) REVERT: D 18 GLN cc_start: 0.9506 (tp40) cc_final: 0.9280 (mt0) REVERT: A 277 ASP cc_start: 0.8681 (t0) cc_final: 0.8241 (t0) REVERT: A 431 ASP cc_start: 0.8375 (t0) cc_final: 0.8056 (t0) REVERT: A 534 TYR cc_start: 0.8400 (p90) cc_final: 0.8182 (p90) REVERT: A 601 ASP cc_start: 0.8807 (p0) cc_final: 0.8305 (t0) REVERT: B 382 GLU cc_start: 0.8574 (tp30) cc_final: 0.8054 (mm-30) REVERT: B 892 HIS cc_start: 0.9348 (OUTLIER) cc_final: 0.9109 (t-170) outliers start: 28 outliers final: 11 residues processed: 87 average time/residue: 0.2054 time to fit residues: 28.1563 Evaluate side-chains 71 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 892 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 25 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN B 432 ASN ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.086438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.060348 restraints weight = 44884.566| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 4.32 r_work: 0.3109 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11441 Z= 0.115 Angle : 0.580 9.339 15491 Z= 0.302 Chirality : 0.043 0.160 1682 Planarity : 0.003 0.053 1991 Dihedral : 5.273 21.078 1502 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 2.01 % Allowed : 14.53 % Favored : 83.47 % 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: -1.63 (0.22), residues: 1336 helix: -0.69 (0.39), residues: 172 sheet: -1.22 (0.32), residues: 260 loop : -1.14 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 924 HIS 0.010 0.001 HIS A 654 PHE 0.016 0.001 PHE B 409 TYR 0.008 0.001 TYR A 606 ARG 0.006 0.000 ARG A 897 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 243) hydrogen bonds : angle 6.53666 ( 648) SS BOND : bond 0.00164 ( 24) SS BOND : angle 0.69781 ( 48) covalent geometry : bond 0.00258 (11417) covalent geometry : angle 0.57970 (15443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9374 (pp) cc_final: 0.9092 (mp) REVERT: D 18 GLN cc_start: 0.9468 (tp-100) cc_final: 0.9261 (mt0) REVERT: A 277 ASP cc_start: 0.8640 (t0) cc_final: 0.8216 (t0) REVERT: A 431 ASP cc_start: 0.8305 (t0) cc_final: 0.8002 (t0) REVERT: A 601 ASP cc_start: 0.8723 (p0) cc_final: 0.8242 (t0) REVERT: A 629 ILE cc_start: 0.9169 (mm) cc_final: 0.8852 (pt) REVERT: A 856 HIS cc_start: 0.9315 (OUTLIER) cc_final: 0.9094 (t-90) outliers start: 25 outliers final: 13 residues processed: 82 average time/residue: 0.1972 time to fit residues: 25.7387 Evaluate side-chains 69 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 639 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 128 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 76 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS B 847 HIS B 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.085841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.059668 restraints weight = 45046.696| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 4.31 r_work: 0.3092 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11441 Z= 0.143 Angle : 0.584 12.804 15491 Z= 0.302 Chirality : 0.043 0.160 1682 Planarity : 0.003 0.037 1991 Dihedral : 5.149 20.582 1502 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 2.09 % Allowed : 15.09 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.22), residues: 1336 helix: -0.78 (0.38), residues: 180 sheet: -1.20 (0.32), residues: 265 loop : -1.17 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 859 HIS 0.010 0.001 HIS A 654 PHE 0.012 0.001 PHE B 409 TYR 0.010 0.001 TYR A 428 ARG 0.009 0.000 ARG B 603 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 243) hydrogen bonds : angle 6.39112 ( 648) SS BOND : bond 0.00204 ( 24) SS BOND : angle 0.67437 ( 48) covalent geometry : bond 0.00326 (11417) covalent geometry : angle 0.58411 (15443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9377 (pp) cc_final: 0.9075 (mp) REVERT: D 18 GLN cc_start: 0.9464 (tp-100) cc_final: 0.9239 (mm-40) REVERT: A 277 ASP cc_start: 0.8641 (t0) cc_final: 0.8203 (t0) REVERT: A 431 ASP cc_start: 0.8329 (t0) cc_final: 0.8050 (t0) REVERT: A 534 TYR cc_start: 0.8368 (p90) cc_final: 0.8167 (p90) REVERT: A 601 ASP cc_start: 0.8732 (p0) cc_final: 0.8225 (t0) REVERT: A 629 ILE cc_start: 0.9104 (mm) cc_final: 0.8795 (pt) REVERT: B 382 GLU cc_start: 0.8494 (tp30) cc_final: 0.7992 (mm-30) outliers start: 26 outliers final: 16 residues processed: 83 average time/residue: 0.1745 time to fit residues: 24.1771 Evaluate side-chains 72 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain B residue 845 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.084109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.057878 restraints weight = 45828.189| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.31 r_work: 0.3050 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11441 Z= 0.263 Angle : 0.661 10.119 15491 Z= 0.341 Chirality : 0.045 0.167 1682 Planarity : 0.004 0.050 1991 Dihedral : 5.454 19.842 1502 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.06 % Favored : 90.87 % Rotamer: Outliers : 2.89 % Allowed : 14.53 % Favored : 82.58 % 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: -1.82 (0.22), residues: 1336 helix: -0.77 (0.39), residues: 173 sheet: -1.56 (0.30), residues: 277 loop : -1.20 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 924 HIS 0.017 0.001 HIS A 856 PHE 0.019 0.002 PHE A 408 TYR 0.017 0.002 TYR A 428 ARG 0.006 0.000 ARG A 897 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 243) hydrogen bonds : angle 6.56731 ( 648) SS BOND : bond 0.00388 ( 24) SS BOND : angle 0.80257 ( 48) covalent geometry : bond 0.00601 (11417) covalent geometry : angle 0.66045 (15443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 58 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 18 GLN cc_start: 0.9445 (tp-100) cc_final: 0.9232 (mm-40) REVERT: A 277 ASP cc_start: 0.8701 (t0) cc_final: 0.8242 (t0) REVERT: A 431 ASP cc_start: 0.8328 (t0) cc_final: 0.8052 (t0) REVERT: A 534 TYR cc_start: 0.8477 (p90) cc_final: 0.8276 (p90) REVERT: A 601 ASP cc_start: 0.8738 (p0) cc_final: 0.8188 (t0) REVERT: A 833 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6370 (pmm) REVERT: B 800 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7542 (pp) outliers start: 36 outliers final: 23 residues processed: 89 average time/residue: 0.2898 time to fit residues: 41.0531 Evaluate side-chains 78 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 857 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 107 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.085389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.059337 restraints weight = 45701.989| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.33 r_work: 0.3084 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11441 Z= 0.116 Angle : 0.581 10.213 15491 Z= 0.302 Chirality : 0.043 0.171 1682 Planarity : 0.003 0.036 1991 Dihedral : 5.224 19.801 1502 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.41 % Favored : 92.51 % Rotamer: Outliers : 2.57 % Allowed : 15.49 % Favored : 81.94 % 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: -1.71 (0.23), residues: 1336 helix: -0.64 (0.39), residues: 173 sheet: -1.49 (0.31), residues: 277 loop : -1.12 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 924 HIS 0.010 0.001 HIS A 654 PHE 0.020 0.001 PHE B 509 TYR 0.010 0.001 TYR C 59 ARG 0.008 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 243) hydrogen bonds : angle 6.35451 ( 648) SS BOND : bond 0.00178 ( 24) SS BOND : angle 0.94807 ( 48) covalent geometry : bond 0.00263 (11417) covalent geometry : angle 0.57999 (15443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9003 (mp) REVERT: A 277 ASP cc_start: 0.8639 (t0) cc_final: 0.8427 (t70) REVERT: A 431 ASP cc_start: 0.8276 (t0) cc_final: 0.8033 (t0) REVERT: A 601 ASP cc_start: 0.8693 (p0) cc_final: 0.8189 (t0) REVERT: A 833 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6379 (pmm) outliers start: 32 outliers final: 19 residues processed: 90 average time/residue: 0.1959 time to fit residues: 27.2675 Evaluate side-chains 77 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 845 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 131 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 122 optimal weight: 0.0570 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 135 optimal weight: 0.0570 chunk 112 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.085899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.059894 restraints weight = 45623.844| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 4.33 r_work: 0.3101 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11441 Z= 0.111 Angle : 0.584 9.952 15491 Z= 0.303 Chirality : 0.043 0.153 1682 Planarity : 0.003 0.045 1991 Dihedral : 5.090 19.482 1502 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.34 % Favored : 92.59 % Rotamer: Outliers : 1.93 % Allowed : 15.81 % Favored : 82.26 % 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: -1.65 (0.23), residues: 1336 helix: -0.57 (0.40), residues: 173 sheet: -1.36 (0.31), residues: 269 loop : -1.13 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 924 HIS 0.010 0.001 HIS A 654 PHE 0.015 0.001 PHE B 509 TYR 0.010 0.001 TYR A 534 ARG 0.011 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 243) hydrogen bonds : angle 6.19363 ( 648) SS BOND : bond 0.00160 ( 24) SS BOND : angle 0.72617 ( 48) covalent geometry : bond 0.00248 (11417) covalent geometry : angle 0.58383 (15443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: D 18 GLN cc_start: 0.9290 (mm-40) cc_final: 0.9052 (mm110) REVERT: A 277 ASP cc_start: 0.8615 (t0) cc_final: 0.8413 (t70) REVERT: A 321 MET cc_start: 0.8469 (pmm) cc_final: 0.8125 (pmm) REVERT: A 431 ASP cc_start: 0.8302 (t0) cc_final: 0.8046 (t0) REVERT: A 601 ASP cc_start: 0.8671 (p0) cc_final: 0.8194 (t0) REVERT: A 833 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.5719 (pmm) REVERT: B 800 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7519 (pp) outliers start: 24 outliers final: 19 residues processed: 85 average time/residue: 0.1961 time to fit residues: 26.3775 Evaluate side-chains 78 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 845 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 89 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 866 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.085774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.059872 restraints weight = 45173.573| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 4.32 r_work: 0.3103 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11441 Z= 0.113 Angle : 0.575 9.700 15491 Z= 0.298 Chirality : 0.043 0.155 1682 Planarity : 0.003 0.037 1991 Dihedral : 5.030 19.913 1502 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.41 % Favored : 92.51 % Rotamer: Outliers : 2.09 % Allowed : 16.21 % Favored : 81.70 % 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: -1.64 (0.23), residues: 1336 helix: -0.42 (0.40), residues: 171 sheet: -1.29 (0.32), residues: 263 loop : -1.19 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 859 HIS 0.010 0.001 HIS A 654 PHE 0.016 0.001 PHE B 509 TYR 0.014 0.001 TYR B 534 ARG 0.008 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 243) hydrogen bonds : angle 6.13755 ( 648) SS BOND : bond 0.00161 ( 24) SS BOND : angle 0.71293 ( 48) covalent geometry : bond 0.00253 (11417) covalent geometry : angle 0.57485 (15443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8451 (pmm) cc_final: 0.8100 (pmm) REVERT: A 431 ASP cc_start: 0.8300 (t0) cc_final: 0.8046 (t0) REVERT: A 601 ASP cc_start: 0.8638 (p0) cc_final: 0.8174 (t0) REVERT: A 833 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6486 (pmm) REVERT: B 800 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7546 (pp) outliers start: 26 outliers final: 24 residues processed: 81 average time/residue: 0.1763 time to fit residues: 23.6975 Evaluate side-chains 82 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain C residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 119 optimal weight: 0.4980 chunk 37 optimal weight: 0.0270 chunk 63 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 104 optimal weight: 0.0970 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN B 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.086065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.060264 restraints weight = 45370.060| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 4.31 r_work: 0.3113 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11441 Z= 0.099 Angle : 0.569 9.623 15491 Z= 0.293 Chirality : 0.043 0.155 1682 Planarity : 0.003 0.037 1991 Dihedral : 4.932 19.360 1502 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.26 % Rotamer: Outliers : 2.09 % Allowed : 16.45 % Favored : 81.46 % 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: -1.59 (0.23), residues: 1336 helix: -0.37 (0.40), residues: 171 sheet: -1.21 (0.31), residues: 272 loop : -1.16 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 859 HIS 0.010 0.001 HIS A 654 PHE 0.012 0.001 PHE B 509 TYR 0.011 0.001 TYR B 534 ARG 0.006 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 243) hydrogen bonds : angle 6.05054 ( 648) SS BOND : bond 0.00139 ( 24) SS BOND : angle 0.67345 ( 48) covalent geometry : bond 0.00218 (11417) covalent geometry : angle 0.56878 (15443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8470 (pmm) cc_final: 0.8127 (pmm) REVERT: A 431 ASP cc_start: 0.8272 (t0) cc_final: 0.8007 (t0) REVERT: A 601 ASP cc_start: 0.8624 (p0) cc_final: 0.8175 (t0) REVERT: A 833 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6494 (pmm) REVERT: B 800 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7544 (pp) outliers start: 26 outliers final: 22 residues processed: 83 average time/residue: 0.1954 time to fit residues: 27.0586 Evaluate side-chains 84 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain C residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 0.6980 chunk 129 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 124 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.086176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.060208 restraints weight = 45272.142| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.31 r_work: 0.3123 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11441 Z= 0.109 Angle : 0.570 9.371 15491 Z= 0.292 Chirality : 0.043 0.157 1682 Planarity : 0.003 0.038 1991 Dihedral : 4.895 19.106 1502 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 2.17 % Allowed : 16.53 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.23), residues: 1336 helix: -0.20 (0.41), residues: 165 sheet: -1.22 (0.32), residues: 265 loop : -1.10 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 859 HIS 0.010 0.001 HIS A 654 PHE 0.017 0.001 PHE B 509 TYR 0.011 0.001 TYR B 534 ARG 0.005 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 243) hydrogen bonds : angle 6.03456 ( 648) SS BOND : bond 0.00159 ( 24) SS BOND : angle 0.65167 ( 48) covalent geometry : bond 0.00247 (11417) covalent geometry : angle 0.56983 (15443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9972.94 seconds wall clock time: 177 minutes 5.16 seconds (10625.16 seconds total)